diff --git a/.github/workflows/claude-code-review.yml b/.github/workflows/claude-code-review.yml deleted file mode 100644 index e8372ebc6..000000000 --- a/.github/workflows/claude-code-review.yml +++ /dev/null @@ -1,79 +0,0 @@ -name: Claude Code Review - -on: - pull_request: - types: [opened, synchronize, reopened] -# # Optional: Only run on specific file changes -# # paths: -# # - "src/**/*.ts" -# # - "src/**/*.tsx" -# # - "src/**/*.js" -# # - "src/**/*.jsx" - -jobs: - claude-review: - # Optional: Filter by PR author - # if: | - # github.event.pull_request.user.login == 'external-contributor' || - # github.event.pull_request.user.login == 'new-developer' || - # github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR' - - runs-on: ubuntu-latest - permissions: - contents: read - pull-requests: write - issues: read - id-token: write - - steps: - - name: Checkout repository - uses: actions/checkout@v4 - with: - fetch-depth: 1 - - - name: Run Claude Code Review - id: claude-review - uses: anthropics/claude-code-action@beta - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }} - - # Optional: Specify model (defaults to Claude Sonnet 4, uncomment for Claude Opus 4.1) - # model: "claude-opus-4-1-20250805" - - # Direct prompt for automated review (no @claude mention needed) - direct_prompt: | - Please review this pull request and provide feedback on: - - Code quality and best practices - - Potential bugs or issues - - Performance considerations - - Security concerns - - Test coverage - - Be constructive and helpful in your feedback. - - # Optional: Use sticky comments to make Claude reuse the same comment on subsequent pushes to the same PR - # use_sticky_comment: true - - # Optional: Customize review based on file types - # direct_prompt: | - # Review this PR focusing on: - # - For TypeScript files: Type safety and proper interface usage - # - For API endpoints: Security, input validation, and error handling - # - For React components: Performance, accessibility, and best practices - # - For tests: Coverage, edge cases, and test quality - - # Optional: Different prompts for different authors - # direct_prompt: | - # ${{ github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR' && - # 'Welcome! Please review this PR from a first-time contributor. Be encouraging and provide detailed explanations for any suggestions.' || - # 'Please provide a thorough code review focusing on our coding standards and best practices.' }} - - # Optional: Add specific tools for running tests or linting - # allowed_tools: "Bash(npm run test),Bash(npm run lint),Bash(npm run typecheck)" - - # Optional: Skip review for certain conditions - # if: | - # !contains(github.event.pull_request.title, '[skip-review]') && - # !contains(github.event.pull_request.title, '[WIP]') - diff --git a/AGENTS.md b/AGENTS.md index 4b26b78b6..29ffc7ff1 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -6,16 +6,16 @@ Schema and generated objects for biolink data model and upper ontology ## Repo management This repo uses `uv` for managing dependencies. Never use commands like `pip` to add or manage dependencies. -`uv run` is the best way to run things, unless you are using `justfile` or `makefile` target +`uv run` is the best way to run things, unless you are using a `makefile` target `mkdocs` is used for documentation.## This is a LinkML Schema repository Layout: - * `src/biolink_model/schema/biolink_model.yaml` - LinkML source schema (edit this) + * `biolink_model.yaml` - LinkML source schema (edit this) * `project` - derived files (do not edit these directly, they are derived from the LinkML) * `src/docs` - source markdown for documentation - * `docs` - derived docs - do not edit these directly + * `docs` - derived docs - do NOT edit these directly * `src/data/examples/{valid,invalid}` - example data files * always include positive examples of each class in the `valid` subfolder * include negative examples for unit tests and to help illustrate pitfalls @@ -24,10 +24,9 @@ Layout: Building and testing: -* `just --list` to see all commands -* `just gen-project` to generate `project` files -* `just test` to test schema and pos/neg examples -* `just lint` analogous to ruff for python +* `make --help` to see all commands +* `make gen-project` to generate `project` files +* `make test` to test schema and pos/neg examples These are wrappers on top of existing linkml commands such as `gen-project`, `linkml-convert`, `linkml-run-examples`. You can run the underlying commands (with `uv run ...`) but in general justfile targets should be favored. @@ -39,5 +38,5 @@ Best practice: * Include meaningful descriptions of each element * always edit biolink-model.yaml in the root of the project. * map to standards where appropriate (e.g. dcterms) -* Never guess OBO term IDs. Always use the OLS MCP to look for relevant ontology terms +* Never guess OBO term IDs. Always use the OLS API to look for relevant ontology terms * be proactive in using due diligence to do deep research on the domain, and look at existing standards diff --git a/Makefile b/Makefile index 95e5a2b7a..3ddf6ab1a 100644 --- a/Makefile +++ b/Makefile @@ -110,7 +110,7 @@ gen-project: $(PYMODEL) # keep these in sync between PROJECT_FOLDERS and the includes/excludes for gen-project and test-schema $(RUN) gen-project \ --exclude excel \ - --include graphql \ + --exclude graphql \ --include jsonld \ --exclude markdown \ --include prefixmap \ @@ -139,7 +139,7 @@ tests: $(RUN) codespell $(RUN) yamllint -c .yamllint-config biolink-model.yaml -test: test-schema test-python test-examples lint spell +test: test-schema test-python lint spell test-schema: gen-project @@ -202,7 +202,6 @@ gendoc: $(DOCDIR) cp $(DEST)/jsonld/biolink_model.context.jsonld $(DOCDIR)/context.jsonld ; \ cp $(DEST)/jsonld/biolink_model.jsonld $(DOCDIR)/biolink-model.jsonld ; \ cp $(DEST)/jsonschema/biolink_model.schema.json $(DOCDIR)/biolink-model.json ; \ - cp $(DEST)/graphql/biolink_model.graphql $(DOCDIR)/biolink-model.graphql ; \ cp $(DEST)/shex/biolink_model.shex $(DOCDIR)/biolink-modeln.shex ; \ cp $(DEST)/shacl/biolink_model.shacl.ttl $(DOCDIR)/biolink-model.shacl.ttl ; \ cp $(DEST)/prefixmap/* $(DOCDIR) ; \ @@ -229,7 +228,7 @@ MKDOCS = $(RUN) mkdocs mkd-%: $(MKDOCS) $* -PROJECT_FOLDERS = sqlschema shex shacl protobuf prefixmap owl jsonschema jsonld graphql excel +PROJECT_FOLDERS = sqlschema shex shacl protobuf prefixmap owl jsonschema jsonld excel git-init-add: git-init git-add git-commit git-status git-init: git init diff --git a/biolink-model.yaml b/biolink-model.yaml index 71311a147..1ed0d6a35 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -214,7 +214,7 @@ types: chemical formula value: uri: xsd:string base: str - description: A chemical formula + description: A type of string representing a chemical formula notes: - Should be implemented as a stronger type @@ -222,36 +222,50 @@ types: uri: xsd:string typeof: uriorcurie description: >- - An IRI + An IRI. label type: uri: xsd:string typeof: string description: >- - A string that provides a human-readable name for an entity + A type of string that provides a human-readable name for an entity. narrative text: uri: xsd:string typeof: string description: >- - A string that provides a human-readable description of something + A type of string that provides a human-readable description of something. symbol type: uri: xsd:string typeof: string + description: >- + A type of string that is typically short, used as a human-readable label or symbol for an entity, + such as an official gene symbol (e.g., "BRCA1") or a chemical symbol. frequency value: typeof: string uri: UO:0000105 + description: >- + A quantity expressing the number of occurrences of a repeating event per + unit of time (UO:0000105). Typically used for rates such as incidence + or event frequency associated with a phenomenon. percentage frequency value: typeof: double uri: UO:0000187 + description: >- + A frequency value expressed as a percentage (UO:0000187), i.e., a + dimensionless ratio multiplied by 100. quotient: aliases: ['ratio'] typeof: double uri: UO:0010006 + description: >- + A dimensionless value obtained by dividing one quantity by another of + the same kind (UO:0010006). Used to represent ratios such as odds + ratios, hazard ratios, or relative risks. unit: typeof: string @@ -260,14 +274,25 @@ types: - UO exact_mappings: - qud:Unit + description: >- + A standard of measurement in which the magnitude of a physical quantity + is expressed (UO:0000000). Typically drawn from the Units of Measurement + Ontology (UO). time type: uri: xsd:string typeof: time + description: >- + A value representing a point in time, serialised as a lexical + representation of xsd:time. biological sequence: uri: xsd:string typeof: string + description: >- + A string of characters representing a biological macromolecule sequence, + such as a nucleic acid sequence (DNA/RNA) using the IUPAC nucleotide + alphabet, or a protein sequence using the IUPAC amino-acid alphabet. ## ------------ ## SLOTS @@ -509,6 +534,10 @@ slots: - WIKIDATA_PROPERTY:P854 type: + description: >- + An rdf:type property asserting that an entity is an instance of a particular class. + In Biolink the value is typically used to indicate the most specific category + of which the entity is an instance. slot_uri: rdf:type domain: entity exact_mappings: @@ -603,6 +632,9 @@ slots: - NCIT:C42677 reaction balanced: + description: >- + Indicates whether a chemical reaction is stoichiometrically balanced, i.e. whether the + conservation of atoms (and charge) holds between the reactants and the products. is_a: association slot range: boolean @@ -645,21 +677,34 @@ slots: - RXNORM:has_tradename exact synonym: + description: >- + An alternate label for an entity that denotes exactly the same meaning as the primary label + and is interchangeable with it in all contexts. is_a: synonym exact_mappings: - oboInOwl:hasExactSynonym broad synonym: + description: >- + An alternate label for an entity whose meaning is broader (more general) than the primary label + but is still useful as a lexical alternative. is_a: synonym exact_mappings: - oboInOwl:hasBroadSynonym narrow synonym: + description: >- + An alternate label for an entity whose meaning is narrower (more specific) than the primary label, + for example naming a particular sub-type. is_a: synonym exact_mappings: - oboInOwl:hasNarrowSynonym related synonym: + description: >- + An alternate label that is related to the primary label but is neither exactly synonymous nor + cleanly broader or narrower; useful as a lexical pointer but not for strict equivalence. + Corresponds to oboInOwl:hasRelatedSynonym. is_a: synonym exact_mappings: - oboInOwl:hasRelatedSynonym @@ -771,10 +816,7 @@ slots: being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge - holds knowledge that was retrieved from multiple sources. e.g. - an Edge provided by the ARAGORN ARA can expressing knowledge it - retrieved from both the automat-mychem-info and molepro KPs, - which both provided it with records of this single fact. + holds knowledge that was retrieved from multiple sources. multivalued: true domain: retrieval source range: uriorcurie @@ -874,6 +916,10 @@ slots: ## Statistics aggregate statistic: + description: >- + An abstract grouping for summary numerical measures (e.g. count, total, quotient, + percentage, rate) computed over a set of observations or a reference population, + used to describe a property of an aggregated entity rather than an individual instance. is_a: node property abstract: true @@ -904,6 +950,8 @@ slots: ## Properties for Information Content Entity and Publication Nodes has taxonomic rank: + description: >- + The taxonomic rank (e.g. species, genus, family, order, kingdom) assigned to an organism taxon. is_a: node property range: taxonomic rank multivalued: false @@ -911,6 +959,8 @@ slots: - WIKIDATA:P105 has dataset: + description: >- + Links a dataset version to the underlying dataset that it is a version of. is_a: node property domain: dataset version range: dataset @@ -918,17 +968,24 @@ slots: - dct:source source web page: + description: >- + A URL of a web page that documents or serves as the landing page for a data source. is_a: node property domain: dataset summary broad_mappings: - dct:source source logo: + description: >- + A URL referencing an image that serves as the visual logo of a data source. is_a: node property domain: dataset summary slot_uri: schema:logo retrieved on: + description: >- + The date on which a dataset was retrieved or harvested from its original source, + following pav:retrievedOn. is_a: node property domain: dataset range: date @@ -936,6 +993,9 @@ slots: - pav:retrievedOn version of: + description: >- + Links a dataset version to the dataset summary of which it is a version, edition, or + adaptation. is_a: node property domain: dataset version range: dataset summary @@ -943,6 +1003,9 @@ slots: - dct:isVersionOf version: + description: >- + A label identifying a particular release or edition of a dataset or resource, typically + following a versioning scheme such as a semantic version string or a release date. is_a: node property domain: dataset broad_mappings: @@ -950,6 +1013,9 @@ slots: - owl:versionInfo license: + description: >- + A legal instrument under which the information content entity is made available, typically + identified by a URL or CURIE pointing to a license document. is_a: node property domain: information content entity exact_mappings: @@ -958,12 +1024,18 @@ slots: - WIKIDATA_PROPERTY:P275 rights: + description: >- + A statement describing rights held in or over the information content entity, such as copyright, + intellectual property, or access and usage rights. is_a: node property domain: information content entity exact_mappings: - dct:rights format: + description: >- + The file format, physical medium, or representational form of the information content entity; + for digital resources typically a MIME type or format identifier. Corresponds to dct:format. is_a: node property domain: information content entity exact_mappings: @@ -971,34 +1043,51 @@ slots: - WIKIDATA_PROPERTY:P2701 created with: + description: >- + An identifier (typically a URL or CURIE) of the software tool, service, or pipeline used + to create the dataset. is_a: node property domain: dataset exact_mappings: - pav:createdWith download url: + description: >- + A URL from which the information content entity may be directly downloaded in its native + serialization. is_a: node property domain: information content entity slot_uri: dcat:downloadURL dataset download url: + description: >- + A URL from which the dataset itself may be directly downloaded specialised for the dataset domain. is_a: node property domain: dataset slot_uri: dcat:downloadURL distribution download url: + description: >- + A URL from which a specific distribution (serialization or format) of a dataset may be directly + downloaded; corresponds to dcat:downloadURL specialised for the dataset distribution domain. is_a: node property domain: dataset distribution exact_mappings: - dcat:downloadURL ingest date: + description: >- + The date on which a dataset version was ingested into the local knowledge graph or downstream + data system; a specialization of dct:issued for the ingestion context. is_a: node property domain: dataset version broad_mappings: - dct:issued has distribution: + description: >- + Links a dataset version to one of its dataset distributions (a specific representation or + serialization of the dataset). is_a: node property domain: dataset version range: dataset distribution @@ -1007,8 +1096,7 @@ slots: published in: is_a: node property description: >- - CURIE identifier of a broader publication context within which the publication may be placed, - e.g. a specified book or journal. + CURIE identifier of a broader publication context within which the publication may be placed. domain: publication range: uriorcurie values_from: @@ -1114,8 +1202,6 @@ slots: Type of exposure domain: exposure event range: string -# range: not sure how standardized this can be made, i.e., into a Biolink Enum. -# To some extent, the subclassing of Exposure Events provides some typing? exposure vehicle: is_a: node property @@ -1123,7 +1209,6 @@ slots: Type of an exposure event. domain: exposure event range: string -# range: not sure how standardized this can be made, i.e., into a Biolink Enum exposure route: is_a: node property @@ -1131,7 +1216,6 @@ slots: Route of exposure. domain: exposure event range: string -# range: not sure how standardized this can be made, i.e., into a Biolink Enum exposure start age: is_a: node property @@ -1159,7 +1243,7 @@ slots: description: >- Magnitude of an exposure event, e.g, parts per million of a toxic chemical. domain: exposure event - range: string # might want to be a more constrained data type here? + range: string exposure additional condition: is_a: node property @@ -1322,6 +1406,9 @@ slots: - OMIM:has_inheritance_type has zygosity: + description: >- + The zygosity characterising a genotype or + nucleic acid entity at a particular locus. is_a: node property domain: nucleic acid entity range: zygosity @@ -1380,7 +1467,8 @@ slots: domain: exposure event range: organismal entity description: >- - the organism or organism part being exposed + An entity that interacts with an exposure stimulus + during an exposure event. exact_mappings: - ExO:0000001 @@ -1389,9 +1477,12 @@ slots: domain: exposure event aliases: ['has stimulus'] description: >- - the process or entity that the receptor is being exposed to + An agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an + exposure_receptor during an exposure event. exact_mappings: - ExO:0000000 + id_prefixes: + - ExO has route: is_a: node property @@ -1442,22 +1533,31 @@ slots: is supplement: description: >- + A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used + as a dietary or nutritional supplement rather than as a conventional drug or food. is_a: node property domain: chemical mixture trade name: description: >- + A proprietary brand or trade name under which a chemical entity (typically a drug) + is manufactured and marketed by a vendor. is_a: node property domain: chemical entity available from: description: >- + The regulatory or commercial availability channel through which a drug or chemical entity + can be obtained, drawn from DrugAvailabilityEnum. is_a: node property multivalued: true range: DrugAvailabilityEnum + examples: + - value: "over_the_counter" is toxic: description: >- + A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure. is_a: node property multivalued: false range: boolean @@ -1466,6 +1566,7 @@ slots: is_a: related to at concept level description: >- A role is particular behaviour which a chemical entity may exhibit. + domain: chemical entity range: chemical role multivalued: true inverse: is chemical role of @@ -1479,6 +1580,9 @@ slots: is_a: related to at concept level description: >- Holds between a chemical role and a chemical entity that exhibits that role. + domain: chemical role + range: chemical entity + multivalued: true inverse: has chemical role max tolerated dose: @@ -1493,6 +1597,8 @@ slots: animal model available from: description: >- + A resource (such as a model organism database) from which an animal model representing the given + disease or phenotypic feature may be obtained. is_a: node property multivalued: true range: disease or phenotypic feature @@ -1523,6 +1629,8 @@ slots: FDA adverse event level: description: >- + The level or severity grade of an adverse event as classified by FDA adverse-event terminology, + drawn from FDAIDAAdverseEventEnum; used on adverse-event associations. is_a: association slot range: FDAIDAAdverseEventEnum @@ -1616,20 +1724,21 @@ slots: and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. examples: - - value: CHEBI:5118 # fluoxetine + - value: CHEBI:5118 description: >- - In a MAXO annotation this would be a specialization in treatment of a disease. For example, + fluoxetine. In a MAXO annotation this would be a specialization in treatment of a disease. For example, fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term 'congenital myasthenic syndrome '4A.' - - value: GO:0005634 # nucleus + - value: GO:0005634 description: >- - In an expression annotation this would be a specialization in location of an anatomical entity. For example, + nucleus. In an expression annotation this would be a specialization in location of an anatomical entity. For example, "expression in the nucleus of hepatic cells" would be a specialization of "expression in hepatic cells" aspect qualifier: is_a: qualifier abstract: true + range: GeneOrGeneProductOrChemicalEntityAspectEnum description: >- Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that @@ -1671,7 +1780,7 @@ slots: abstract: true description: >- defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can - use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). + use to directly represent it). examples: - value: polyA tail - value: upstream control region @@ -1684,8 +1793,8 @@ slots: description: >- Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs. examples: - - value: cohort x (e.g. a specific population, referenced by an identifier) - - value: gut microbiome # OHMI:0000020 + - value: OHMI:0000020 + description: gut microbiome in_subset: - translator_minimal @@ -1781,8 +1890,11 @@ slots: subject part qualifier: description: >- defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can - use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the + use to directly represent it). This qualifier is for the subject of an association (or statement). + examples: + - value: polyA tail + - value: upstream control region is_a: part qualifier in_subset: - translator_minimal @@ -1800,6 +1912,8 @@ slots: - translator_minimal subject context qualifier: + description: >- + A qualifier describing the context in which the subject of an association holds. is_a: context qualifier in_subset: - translator_minimal @@ -1808,6 +1922,9 @@ slots: description: >- Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement). + examples: + - value: increased + - value: downregulated is_a: direction qualifier range: DirectionQualifierEnum in_subset: @@ -1858,8 +1975,11 @@ slots: object part qualifier: description: >- defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can - use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the + use to directly represent it). This qualifier is for the object of an association (or statement). + examples: + - value: polyA tail + - value: upstream control region is_a: part qualifier in_subset: - translator_minimal @@ -1877,6 +1997,8 @@ slots: - translator_minimal object context qualifier: + description: >- + A qualifier describing the context in which the object of an association holds. is_a: context qualifier in_subset: - translator_minimal @@ -1885,6 +2007,9 @@ slots: description: >- Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement). + examples: + - value: increased + - value: downregulated is_a: direction qualifier range: DirectionQualifierEnum in_subset: @@ -1900,6 +2025,9 @@ slots: This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading. + examples: + - value: biolink:causes + description: used with `affects` predicate to express causal statements range: uriorcurie notes: >- to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read @@ -1922,8 +2050,10 @@ slots: is_a: statement qualifier description: >- A statement qualifier representing a type of molecular control mechanism through which an - effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', - 'allosteric modulation', 'channel blocker') + effect of a chemical on a gene or gene product is mediated + examples: + - value: agonism + - value: inhibition range: CausalMechanismQualifierEnum in_subset: - translator_minimal @@ -1937,11 +2067,13 @@ slots: Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ combines with a core concept of ‘neuron’ to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies - taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values - here, the examples below are intended to help clarify the content of the CURIEs. + taxonomic context. Ontology CURIEs are expected as values here, the examples below are intended to help + clarify the content of the CURIEs. examples: - - value: blood # UBERON:0000178 - - value: cerebral cortext # UBERON:0000956 + - value: UBERON:0000178 + description: blood + - value: UBERON:0000956 + description: cerebral cortex in_subset: - translator_minimal multivalued: true @@ -1953,8 +2085,10 @@ slots: expressed in an association took place. range: organism taxon examples: - - value: zebrafish # NCBITaxon:7955 - - value: human # NCBITaxon:9606 + - value: NCBITaxon:7955 + description: zebrafish + - value: NCBITaxon:9606 + description: human notes: - Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs. in_subset: @@ -1966,8 +2100,10 @@ slots: A context qualifier representing a disease or condition in which a relationship expressed in an association took place. range: disease examples: - - value: MONDO:0004979 # Asthma - - value: MONDO:0005148 # type 2 diabetes mellitus + - value: MONDO:0004979 + description: asthma + - value: MONDO:0005148 + description: type 2 diabetes mellitus in_subset: - translator_minimal @@ -2340,8 +2476,7 @@ slots: a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from - different ontological perspectives (e.g. drug as a type of chemical - entity versus drug as a type of role borne by a chemical entity). + different ontological perspectives. in_subset: - translator_minimal symmetric: true @@ -2518,6 +2653,9 @@ slots: range: gene active in: + description: >- + Holds between a gene or gene product and a cellular component in which it carries out its + molecular function. is_a: related to at instance level domain: gene or gene product range: cellular component @@ -2533,6 +2671,10 @@ slots: range: gene or gene product acts upstream of: + description: >- + Holds between a gene or gene product and a biological process such that the molecular function + of the gene product, by way of a chain of causally linked events, is upstream of and + contributes to the execution of the process. is_a: related to at instance level domain: gene or gene product range: biological process @@ -2548,6 +2690,10 @@ slots: range: gene or gene product acts upstream of positive effect: + description: >- + Holds between a gene or gene product and a biological process where the molecular function + of the gene product is upstream of and has a positive (activating or increasing) effect on + the execution of the process. is_a: acts upstream of domain: gene or gene product range: biological process @@ -2563,6 +2709,10 @@ slots: range: gene or gene product acts upstream of negative effect: + description: >- + Holds between a gene or gene product and a biological process where the molecular function + of the gene product is upstream of and has a negative (inhibiting or decreasing) effect on + the execution of the process. is_a: acts upstream of domain: gene or gene product range: biological process @@ -2578,6 +2728,10 @@ slots: range: gene or gene product acts upstream of or within: + description: >- + Holds between a gene or gene product and a biological process when the gene product either + acts upstream of the process or participates in it; used when the more specific causal + relationship is not known. Corresponds to RO:0002264. is_a: acts upstream of domain: gene or gene product range: biological process @@ -2593,6 +2747,10 @@ slots: range: gene or gene product acts upstream of or within positive effect: + description: >- + Holds between a gene or gene product and a biological process when the gene product acts + upstream of or within the process with a positive (activating or increasing) effect on its + execution. Corresponds to RO:0004032. is_a: acts upstream of or within domain: gene or gene product range: biological process @@ -2608,6 +2766,10 @@ slots: range: gene or gene product acts upstream of or within negative effect: + description: >- + Holds between a gene or gene product and a biological process when the gene product acts + upstream of or within the process with a negative (inhibiting or decreasing) effect on its + execution. Corresponds to RO:0004033. is_a: acts upstream of or within domain: gene or gene product range: biological process @@ -2643,6 +2805,11 @@ slots: ## Publication related predicates contributor: + description: >- + Links an information content entity (such as a dataset, publication, or software artefact) to + an agent responsible for making contributions to it. Used as an abstract grouping predicate + over more specific contribution roles (author, editor, publisher, provider). Corresponds to + dct:contributor. is_a: related to at instance level domain: agent range: information content entity @@ -2661,7 +2828,7 @@ slots: provider: is_a: contributor description: >- - person, group, organization or project that provides a piece of information (e.g. a knowledge association). + person, group, organization or project that provides a piece of information. has provider: inverse: provider @@ -2819,6 +2986,9 @@ slots: - DGIdb:binder indirectly physically interacts with: + description: >- + Holds between two entities that physically interact by way of one or more intermediary + entities, rather than through direct physical contact. is_a: physically interacts with symmetric: true annotations: @@ -2951,21 +3121,6 @@ slots: aspect qualifiers). annotations: canonical_predicate: true - comments: >- - subject: NCBIGene:2064 # HER2 - subject_aspect: Amplification - predicate: associated with response to - object: CHEBI:10035 # Trastuzumab - response_type_qualifier: therapeutic_sensitivity - response_direction_qualifer: increased - response_target_qualifier: human patient - disease_context_qualifier: MONDO:0007254 # breast cancer - - subject: MONDO:0007254 - predicate: associated with response to - qualified_predicate: associated with - object: CHEBI:10035 # Trastuzumab - response_context_qualifier: therapeutic_sensitivity response associated with: is_a: associated with @@ -3077,8 +3232,7 @@ slots: is_a: related to at instance level description: >- holds between two chemical entities or genes or gene products where the action of one affects - the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular component, - macromolecular machine mixin, biological or pathological process) to the other. + the susceptibility/sensitivity of a biological entity or system to the other. in_subset: - translator_minimal domain: chemical entity or gene or gene product @@ -3099,8 +3253,7 @@ slots: increases sensitivity to: description: >- holds between two chemical entities or genes or gene products where the action or effect of one - increases the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular - component, macromolecular machine mixin, biological or pathological process) to the other + increases the susceptibility/sensitivity of a biological entity or system to the other is_a: affects sensitivity to in_subset: - translator_minimal @@ -3123,8 +3276,7 @@ slots: decreases sensitivity to: description: >- holds between two chemical entities or genes or gene products where the action or effect of one - decreases the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular - component, macromolecular machine mixin, biological or pathological process) to the other + decreases the susceptibility/sensitivity of a biological entity or system to the other is_a: affects sensitivity to in_subset: - translator_minimal @@ -3570,8 +3722,8 @@ slots: description: >- holds between two genes or gene products that are expressed in the same cell type or population is_a: coexists with - domain: gene or gene product range: gene or gene product + domain: gene or gene product in_subset: - translator_minimal symmetric: true @@ -3601,6 +3753,8 @@ slots: genetically associated with: is_a: associated with description: >- + A statistical association, observed in genetic studies, between a genetic entity such as a gene, locus, or + variant and a phenotype, disease, or trait. symmetric: true annotations: canonical_predicate: true @@ -4063,7 +4217,7 @@ slots: patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS where patients directly report the condition for which they took a drug, or statements from a database cataloging - instances of off-label prescription of drugs for specific conditions (e.g. here, here, here). + instances of off-label prescription of drugs for specific conditions. mixins: - treats or applied or studied to treat domain: chemical or drug or treatment @@ -4186,8 +4340,8 @@ slots: description: >- holds between any two genes or gene products, in which both are generally expressed within a single defined experimental context. - domain: gene or gene product range: gene or gene product + domain: gene or gene product symmetric: true annotations: canonical_predicate: true @@ -4785,6 +4939,10 @@ slots: - SNOMED:has_recipient_category catalyzes: + description: >- + Holds between a macromolecular machine (typically an enzyme or ribozyme) and a biochemical + reaction or process whose rate it accelerates, without itself being consumed, by lowering + the activation energy. is_a: participates in annotations: canonical_predicate: true @@ -4796,6 +4954,9 @@ slots: inverse: catalyzes has substrate: + description: >- + Holds between a biochemical reaction or catalytic process and a chemical entity that is + acted upon (consumed or transformed) by that reaction. is_a: has participant domain: chemical entity or gene or gene product range: chemical entity or gene or gene product @@ -5158,6 +5319,9 @@ slots: - RO:0003001 consumes: + description: >- + Holds between a process and an entity that is taken in and depleted by the process; for + example a metabolite consumed in a biochemical reaction. is_a: has input domain: named thing range: named thing @@ -5261,6 +5425,9 @@ slots: inverse: has variant part related condition: + description: >- + Links a genotype or genetic variant to a condition (disease or phenotypic feature) that is + associated with it. is_a: related to at instance level symmetric: true annotations: @@ -5547,6 +5714,9 @@ slots: - NCIT:C16798 has increased amount: + description: >- + Holds between an entity and a component that is present at higher amount + than in a reference state or sibling entity; used for comparative compositional statements. is_a: related to at instance level annotations: canonical_predicate: true @@ -5559,6 +5729,9 @@ slots: inverse: has increased amount has decreased amount: + description: >- + Holds between an entity and a component that is present at lower amount + than in a reference state or sibling entity; used for comparative compositional statements. is_a: related to at instance level annotations: canonical_predicate: true @@ -5571,6 +5744,10 @@ slots: inverse: has decreased amount lacks part: + description: >- + Holds between an entity and a component that is absent from it relative to a reference type; + for example a cell type lacking a particular organelle or a protein lacking a particular + domain. Corresponds to CL:lacks_part / PR:lacks_part. is_a: related to at instance level annotations: canonical_predicate: true @@ -5586,6 +5763,10 @@ slots: inverse: lacks part develops from: + description: >- + Holds between two entities where the first develops, by one or more developmental processes, + from the second; for example a cell type developing from a precursor cell type or a tissue + developing from an embryonic primordium. Corresponds to RO:0002202. is_a: related to at instance level annotations: canonical_predicate: true @@ -6215,7 +6396,7 @@ slots: dataset count: is_a: association slot description: >- - The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort. + The total number of instances in a dataset/cohort. range: integer examples: - value: 100000 @@ -6311,7 +6492,7 @@ slots: multivalued: true range: string examples: - - value: The administration of 50g/ml bupivacaine promoted maximum breast cancer. + - value: "Here, we report two new cases of rivaroxaban-induced hepatitis." supporting documents: deprecated: true @@ -6331,7 +6512,7 @@ slots: to the subject concept of the extracted assertion. range: integer examples: - - value: 15 + - value: 33 multivalued: true object location in text: @@ -6341,7 +6522,7 @@ slots: to the object concept of the extracted assertion range: integer examples: - - value: 15 + - value: 53 multivalued: true extraction confidence score: @@ -6352,7 +6533,7 @@ slots: assuming that the actual value was the result of chance alone. range: float examples: - - value: "15.0" + - value: "0.6188385904738642" supporting document type: is_a: association slot @@ -6370,7 +6551,7 @@ slots: document used in a Text Mining Result. range: integer examples: - - value: 1999 + - value: 2018 supporting text section type: is_a: association slot @@ -6380,7 +6561,7 @@ slots: (e.g., Abstract, Introduction) that contains the supporting text. range: string examples: - - value: Introduction + - value: abstract ln ratio: is_a: association slot @@ -6641,8 +6822,7 @@ slots: supporting study cohort: is_a: supporting study metadata description: >- - A description of a study population/cohort that was interrogated to provide evidence for the association - (e.g. the inclusion and exclusion criteria). + A description of a study population/cohort that was interrogated to provide evidence for the association. range: string supporting study date range: @@ -6655,7 +6835,7 @@ slots: is_a: supporting study metadata description: >- A term or terms describing the experimental setting/context in which evidence supporting the Association was - generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue + generated ('context' may be defined by many factors, including taxon, model system, tissue type, disease, etc.). range: string @@ -6716,7 +6896,8 @@ slots: - value: text_mining_agent has biological sex: - description: The biological sex of the entity (e.g., male or female) regarding a case description from a phenopacket + description: >- + The biological sex of the entity regarding a case description from a phenopacket required: false range: biological sex @@ -6727,17 +6908,27 @@ slots: classes: # Add the KGX-specific classes without modifying biolink classes KnowledgeGraph: - description: A knowledge graph represented in KGX format + description: >- + A container representing a knowledge graph serialized in KGX (Knowledge Graph Exchange) format. + A KnowledgeGraph aggregates a collection of nodes (entities) and edges (relationships between + entities) conforming to the KGX specification, enabling interoperable exchange of biomedical + knowledge graphs across tools and systems in the Biolink ecosystem. slots: - nodes - edges - Node: - description: A node in a KGX graph, will be superclass for named thing - + description: >- + A generic node in a KGX-formatted knowledge graph, representing a single entity or concept + with a unique identifier. This class serves as the structural superclass for `named thing` + in Biolink, providing the minimal KGX-compliant contract (identifier, category, etc.) that + any biolink entity participating in a knowledge graph must satisfy. Edge: - description: An edge in a KGX graph, will be superclass for association - + description: >- + A generic edge in a KGX-formatted knowledge graph, representing a directed relationship + between a subject node and an object node qualified by a predicate. This class serves as + the structural superclass for `association` in Biolink, providing the minimal KGX-compliant + contract (subject, predicate, object, and associated metadata) that any biolink relationship + participating in a knowledge graph must satisfy. knowledge graph: description: >- @@ -6753,7 +6944,10 @@ classes: mapping collection: description: >- - A collection of deprecated mappings. + An abstract container class that holds a set of predicate mappings. + Serves as a top-level root for documents that enumerate how + third-party or deprecated predicates should be rewritten to Biolink + predicates and their associated qualifiers. abstract: true slots: - predicate mappings @@ -6841,17 +7035,6 @@ classes: - has unit - has numeric value - # Alignment attempted of the biolink:Attribute model - # to the proposed TRAPI Release 1.1 Attribute schema, i.e. - # - # attribute_name: "assertionAuthoredBy", - # attribute_type: SEPIO:0000130, - # value: "ORCID:12345", - # value_type: "wd:Q51044", - # value_type_name: "ORCID ID" - # url: https://orcid.org/12345 - # source: ORCID - attribute: is_a: named thing mixins: @@ -6893,9 +7076,14 @@ classes: exact_mappings: - CHEBI:51086 examples: - - value: CHEBI:35469 # antidepressant role + - value: CHEBI:35469 + description: antidepressant role biological sex: + description: >- + An organismal quality inhering in a bearer by virtue of the bearer's + ability to undergo sexual reproduction in order to differentiate + the individuals or types involved. is_a: attribute exact_mappings: - PATO:0000047 @@ -6923,13 +7111,24 @@ classes: describes the severity of a phenotypic feature or disease relationship quantifier: + description: >- + A mixin for quantifying aspects of the strength, frequency, or + specificity of a relationship between two entities. mixin: true sensitivity quantifier: + description: >- + A relationship quantifier that measures the sensitivity of a + relationship, such as the proportion of true positives correctly + identified in a diagnostic or association context. is_a: relationship quantifier mixin: true specificity quantifier: + description: >- + A relationship quantifier that measures the specificity of a + relationship, such as the proportion of true negatives correctly + identified in a diagnostic or association context. is_a: relationship quantifier mixin: true @@ -6941,6 +7140,9 @@ classes: mixin: true frequency quantifier: + description: >- + A relationship quantifier that expresses how often a relationship + holds, using count, total, quotient, or percentage measures. is_a: relationship quantifier mixin: true slots: @@ -6948,8 +7150,17 @@ classes: - has total - has quotient - has percentage + examples: + - object: + has_count: 42 + has_total: 100 + has_quotient: 0.42 + has_percentage: 42.0 chemical or drug or treatment: + description: >- + A mixin for entities that represent chemical substances, + pharmacological agents, or therapeutic interventions. mixin: true id_prefixes: - PUBCHEM.COMPOUND @@ -7058,6 +7269,8 @@ classes: ## Administrative Entities administrative entity: + description: >- + An entity that is the byproduct of an administrative process. is_a: named thing abstract: true @@ -7115,6 +7328,21 @@ classes: - supporting document type - supporting document year - supporting text section type + examples: + - object: + id: tmkp:id + category: biolink:TextMiningStudyResult + supporting_text: + - "Here, we report two new cases of rivaroxaban-induced hepatitis." + subject_location_in_text: + - 33 + - 44 + object_location_in_text: + - 53 + - 62 + extraction_confidence_score: 0.6188385904738642 + supporting_document_year: 2018 + supporting_text_section_type: abstract icees study result: is_a: study result @@ -7343,8 +7571,7 @@ classes: web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if - of significant knowledge scope (e.g. a figure, figure legend, or section - highlighted by NLP). + of significant knowledge scope. slots: - authors - pages @@ -7411,6 +7638,9 @@ classes: - model_organism_database book chapter: + description: >- + A section of a book that forms a discrete unit of a larger + published work and may be independently authored or cited. is_a: publication slots: - published in @@ -7564,6 +7794,14 @@ classes: One or more URLs that link to a specific web page or document provided by the InformationResource, that contains a record of the knowledge expressed in the Edge. + examples: + - object: + id: urn:uuid:id + category: biolink:RetrievalSource + resource_id: infores:text-mining-provider-targeted + resource_role: primary_knowledge_source + upstream_resource_ids: + - infores:pubmed ## Top Level Abstractions of Material & Process Entities @@ -7660,8 +7898,10 @@ classes: - STY:T061 # Molecular Biology Research Technique - STY:T063 + - MAXO:0000001 id_prefixes: - CPT + - MAXO phenomenon: is_a: named thing @@ -7751,6 +7991,9 @@ classes: Any entity or process that exists at the level of the whole planet environmental process: + description: >- + A process that occurs within or involves the components of an + environmental system. is_a: planetary entity mixins: - occurrent @@ -7758,6 +8001,9 @@ classes: - ENVO:02500000 environmental feature: + description: >- + A system or entity in the natural environment that has the + disposition to environ one or more material entities. is_a: planetary entity exact_mappings: - ENVO:01000254 @@ -7795,6 +8041,9 @@ classes: - in taxon label biological entity: + description: >- + A heterogeneous substance that contains genomic material or is the + product of a biological process. is_a: named thing aliases: ['bioentity'] abstract: true @@ -7809,6 +8058,9 @@ classes: - STY:T129 # (imft, full name: Immunologic Factor genomic entity: + description: >- + A generically dependent continuant that carries biological + sequence that is part of or derived from a genome. mixin: true slots: - has biological sequence @@ -7819,6 +8071,10 @@ classes: - GENO:0000897 # Genomic Entity epigenomic entity: + description: >- + A mixin for entities that represent epigenomic modifications + or features associated with heritable changes in gene expression + that do not involve changes to the DNA sequence itself. mixin: true slots: - has biological sequence @@ -8275,6 +8531,10 @@ classes: - UMLS pathway: + description: >- + A hierarchical ordering of connected molecular reactions (steps) + that represent a specific biological process, such as signaling + or metabolism. is_a: biological process mixins: - ontology class @@ -8298,6 +8558,8 @@ classes: - ncats.bioplanet physiological process: + description: >- + A biological or chemical function within a living organism. aliases: ['physiology'] is_a: biological process mixins: @@ -8321,6 +8583,10 @@ classes: - REACT behavior: + description: >- + The internally coordinated responses (actions or inactions) of + organisms (individuals or groups) to internal or external stimuli, + via a mechanism that involves nervous system activity. is_a: biological process mixins: - ontology class @@ -8429,7 +8695,12 @@ classes: ## Food environmental food contaminant: + description: >- + Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate + foodstuffs during their production, transportation or storage. is_a: chemical entity + exact_mappings: + - CHEBI:78299 related_mappings: # substance role - CHEBI:78299 @@ -8461,7 +8732,11 @@ classes: - UMLS food additive: + description: >- + Any substance which is added to food to preserve or enhance its flavour and/or appearance. is_a: chemical entity + exact_mappings: + - CHEBI:64047 related_mappings: # substance role - CHEBI:64047 @@ -8495,7 +8770,12 @@ classes: food: is_a: chemical mixture description: >- - A substance consumed by a living organism as a source of nutrition + A substance of plant, animal, or artificial origin consumed by a living organism to provide essential + nutrients, energy, and support growth and the processes of life, or to satisfy other health needs or + provide a social or organoleptic experience. + exact_mappings: + - CHEBI:33290 + - FOODON:00002403 id_prefixes: - foodb.food - foodb.compound @@ -8540,18 +8820,19 @@ classes: aliases: ['phenotypic properties'] is_a: organism attribute description: >- - A property of a phenotype + A characteristic of a phenotype (e.g., weight, size, shape, color) that can be observed, measured, or + compared across organisms or conditions. examples: - - value: weight - mappings: - - PATO:0000001 + - value: "PATO:0000128" + broad_mappings: + - PATO:0001995 genetic inheritance: aliases: ['inheritance'] is_a: biological entity description: >- The pattern or 'mode' in which a particular genetic trait or disorder is passed from one - generation to the next, e.g. autosomal dominant, autosomal recessive, etc. + generation to the next. exact_mappings: - HP:0000005 - GENO:0000141 @@ -8603,6 +8884,8 @@ classes: description: >- A virus is a microorganism that replicates itself as a microRNA and infects the host cell. + comments: >- + see: https://github.com/OBOFoundry/COB/pull/211 exact_mappings: - NCBITaxon:10239 - STY:T005 # Virus @@ -8612,17 +8895,19 @@ classes: mixins: - subject of investigation description: >- + An organism that contains one or more cells belonging to the cellular lineages of life (Archaea, Bacteria, or + Eukaryota), whose body consists of one or more cells. Distinguished from acellular biological entities such as + viruses and viroids. + comments: >- + see: https://github.com/OBOFoundry/COB/pull/211 exact_mappings: - NCBITaxon:131567 mammal: + deprecated: true is_a: cellular organism mixins: - subject of investigation - description: >- - A member of the class Mammalia, a clade of endothermic amniotes - distinguished from reptiles and birds by the possession of hair, - three middle ear bones, mammary glands, and a neocortex exact_mappings: - NCBITaxon:40674 # mammal - STY:T015 # mammal @@ -8630,11 +8915,10 @@ classes: - FOODON:03411134 # mammal human: + deprecated: true is_a: mammal mixins: - subject of investigation - description: >- - A member of the the species Homo sapiens. exact_mappings: - STY:T016 - NCBITaxon:9606 @@ -8642,8 +8926,8 @@ classes: - NCIT:C14225 plant: + deprecated: true is_a: cellular organism - description: >- exact_mappings: - NCIT:C14258 # plant - STY:T002 # plant @@ -8651,9 +8935,8 @@ classes: - NCIT:C79659 # plant, whole invertebrate: + deprecated: true is_a: cellular organism - description: >- - An animal lacking a vertebral column. This group consists of 98% of all animal species. exact_mappings: - NCIT:C14228 # invertebrate - OMIT:0008565 # invertebrates @@ -8663,9 +8946,8 @@ classes: - NCBITaxon:1767184 # unidentified invertebrate vertebrate: + deprecated: true is_a: cellular organism - description: >- - A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column. exact_mappings: - STY:T010 - NCBITaxon:7742 # vertebrata @@ -8674,12 +8956,8 @@ classes: - NCBITaxon:2662825 # unclassified vertebrata (in:vertebrates) fungus: + deprecated: true is_a: cellular organism - description: >- - A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, - including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or - asexually, and have life cycles that range from simple to complex. Filamentous - fungi refer to those that grow as multicellular colonies (mushrooms and molds). exact_mappings: - STY:T004 - NCIT:C14209 @@ -8713,8 +8991,9 @@ classes: individual organism: aliases: ['organism'] description: >- - An instance of an organism. For example, Richard Nixon, - Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576 + An instance of an organism. For example, Charles Darwin, my pet cat. + examples: + - value: ORCID:0000-0002-5355-2576 is_a: organismal entity mixins: - subject of investigation @@ -8759,22 +9038,20 @@ classes: slots: - inheritance description: >- - Either one of a disease or an individual phenotypic feature. - Some knowledge resources such as Monarch treat these as - distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model - for their independent descriptions. This class is helpful to enforce domains and ranges - that may involve either a disease or a phenotypic feature. - narrow_mappings: + A disease or an individual phenotypic feature, grouped as a single class to accommodate source vocabularies + and assertions that do not distinguish the two. Prefer the more specific subclasses disease or phenotypic + feature when the distinction is known. + related_mappings: # UMLS Semantic Type "Finding" - more specialized use of 'disease or phenotypic feature' - STY:T033 disease: aliases: ['condition', 'disorder', 'medical condition'] description: >- - A disorder of structure or function, especially one that produces specific + A disease is a disposition to undergo pathological processes that exists in an organism because of one or + more disorders in that organism. A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a - direct result of physical injury. A disposition to undergo pathological processes that exists in an - organism because of one or more disorders in that organism. + direct result of physical injury. is_a: disease or phenotypic feature exact_mappings: - MONDO:0000001 @@ -8827,7 +9104,7 @@ classes: is_a: disease or phenotypic feature description: >- A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an - individual resulting from the interaction of its genotype with its molecular and physical environment. + individual often resulting from the interaction of its genotype with its molecular and physical environment. examples: - value: MP:0001262 description: decreased body weight @@ -8890,7 +9167,16 @@ classes: - physical essence - ontology class description: >- - A subcellular location, cell type or gross anatomical part + A part of a cellular organism at or above the granularity of a protein complex. This is a grouping class + with three concrete subclasses that should be preferred when applicable: "biolink:Cell" for whole cells, + "biolink:CellularComponent" for subcellular and intracellular structures (organelles, membranes, bacterial + flagella, etc.), and "biolink:GrossAnatomcialStructure" for multicellular parts (tissues, organs, body parts). + Excludes viral and other acellular biological entities. + examples: + - value: UBERON:0000178 + description: blood + - value: UBERON:0002553 + description: anatomical cavity exact_mappings: - UBERON:0001062 - WIKIDATA:Q4936952 @@ -8935,6 +9221,17 @@ classes: is_a: anatomical entity description: >- A location in or around a cell + examples: + - value: GO:0005739 + description: mitochondrion + - value: GO:0005634 + description: nucleus + - value: GO:0005886 + description: plasma membrane + - value: GO:0009288 + description: bacterial-type flagellum + - value: GO:0031012 + description: extracellular matrix exact_mappings: - GO:0005575 - SIO:001400 @@ -8953,7 +9250,16 @@ classes: - UBERON cell: + description: >- + The basic structural and functional unit of all organisms. + Includes the plasma membrane and any external encapsulating + structures such as the cell wall and cell envelope. is_a: anatomical entity + examples: + - value: CL:0000540 + description: neuron + - value: CL:0000236 + description: B cell exact_mappings: - GO:0005623 - CL:0000000 @@ -8973,6 +9279,10 @@ classes: - MESH cell line: + description: >- + A cultured cell population that is genetically stable and + homogeneous, sharing a common propagation history through + successive passages in culture. is_a: organismal entity mixins: - subject of investigation @@ -8982,8 +9292,23 @@ classes: - CLO gross anatomical structure: + description: >- + An anatomical structure that has more than one cell as a part. aliases: ['tissue', 'organ'] is_a: anatomical entity + examples: + - value: UBERON:0000955 + description: brain + - value: UBERON:0002107 + description: liver + - value: UBERON:0000479 + description: tissue + - value: PO:0009046 + description: flower + - value: PO:0009025 + description: leaf + - value: FAO:0001001 + description: hypha exact_mappings: - UBERON:0010000 - WIKIDATA:Q4936952 @@ -9048,10 +9373,11 @@ classes: - DRUGBANK:target gene or gene product or gene family: + is_a: macromolecular machine mixin description: >- A union of gene family or gene loci or gene products, useful to define the association between a gene or gene product or gene family and - some other general class of entity (e.g. biological process or anatomical entity) + some other general class of entity. mixin: true gene: @@ -9063,6 +9389,7 @@ classes: is_a: biological entity mixins: - gene or gene product + - gene or gene product or gene family - genomic entity - chemical entity or gene or gene product - physical essence @@ -9157,8 +9484,8 @@ classes: nucleosome modification: is_a: biological entity description: >- - A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. - e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A. + A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a + variant histone isoform. mixins: - gene product isoform mixin - genomic entity @@ -9207,6 +9534,9 @@ classes: - model_organism_database coding sequence: + description: >- + A contiguous sequence which begins with, and includes, a start + codon and ends with, and includes, a stop codon. is_a: biological entity mixins: - genomic entity @@ -9273,7 +9603,9 @@ classes: is_a: protein description: >- Represents a protein that is a specific isoform of the canonical or - reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ + reference protein. + comments: >- + See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ mixins: - gene product isoform mixin id_prefixes: @@ -9288,7 +9620,6 @@ classes: A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. - e.g. an SH3 domain. mixins: - gene grouping mixin - chemical entity or gene or gene product @@ -9300,13 +9631,26 @@ classes: posttranslational modification: is_a: biological entity description: >- - A chemical modification of a polypeptide or protein that occurs after translation. - e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, - protein ubiquitination. + A chemical modification of a polypeptide or protein that occurs after translation, + altering its structure, activity, localization, or interactions. mixins: - gene product isoform mixin + id_prefixes: + - MOD + - UNIMOD + exact_mappings: + - MOD:00000 # protein modification (PSI-MOD root) + examples: + - value: MOD:00696 + description: phosphorylated residue + - value: MOD:01148 + description: ubiquitinylated lysine protein family: + description: >- + A set of proteins coding for diverse functions which, by virtue + of their high degree of sequence similarity, are believed to have + evolved from a single ancestral gene. is_a: biological entity exact_mappings: - NCIT:C26004 @@ -9324,22 +9668,27 @@ classes: is_a: biological entity description: >- A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, - a biological significance. e.g. the TATA box promoter motif, transcription factor binding + a biological significance. consensus sequences. RNA product: is_a: transcript + description: >- + High molecular weight, linear polymers, composed of nucleotides containing ribose and + linked by phosphodiester bonds typically synthesized by a DNA- or RNA-dependent RNA polymerase that constitutes + the product of a gene. Distinct in emphasis from `biolink:Transcript`, which denotes the informational output of + transcription at the gene-model level rather than the chemical species itself. + examples: + - value: RNACENTRAL:URS00005EB5B7_9606 + - value: mirbase:MI0000060 mixins: - gene product mixin exact_mappings: - - CHEBI:33697 - # This SIO term here also mapped to 'biolink:Transcript'; however, - # since this 'biolink:RNAProduct' relates more to the biochemical - # essence of RNA, then map the SIO term instead to 'biolink:Transcript' - # - SIO:010450 - - WIKIDATA:Q11053 + - CHEBI:33697 # ribonucleic acid + - WIKIDATA:Q11053 # RNA id_prefixes: - RNACENTRAL + - mirbase RNA product isoform: is_a: RNA product @@ -9351,6 +9700,9 @@ classes: - RNACENTRAL noncoding RNA product: + description: >- + An RNA transcript that does not encode for a protein rather the + RNA molecule is the functional gene product. is_a: RNA product id_prefixes: - RNACENTRAL @@ -9361,6 +9713,13 @@ classes: - SIO:001235 microRNA: + description: >- + A small (~22 nucleotide) RNA molecule that is the endogenous + transcript of a miRNA gene. Produced from precursor molecules + that form hairpin structures, which are processed (typically + via the Dicer pathway) to yield a single miRNA molecule. + miRNAs function by triggering cleavage of target molecules + or acting as translational repressors. is_a: noncoding RNA product exact_mappings: - SO:0000276 @@ -9370,6 +9729,7 @@ classes: - MIR - HGNC - WormBase + - mirbase in_subset: - model_organism_database @@ -9414,6 +9774,7 @@ classes: - WIKIDATA:Q417841 mixins: - gene grouping mixin + - gene or gene product or gene family - chemical entity or gene or gene product description: >- any grouping of multiple genes or gene products related by common descent @@ -9442,6 +9803,10 @@ classes: - model_organism_database zygosity: + description: >- + An allelic state describing the degree of similarity between + features at a single locus, specifically whether alleles at the + same location on paired chromosomes are identical or different. is_a: attribute exact_mappings: - GENO:0000133 @@ -9668,6 +10033,9 @@ classes: - CLINICALTRIALS clinical intervention: + description: >- + A medical procedure, treatment, or action taken by healthcare + professionals to modify the course of a disease or condition. is_a: clinical entity clinical finding: @@ -9685,6 +10053,9 @@ classes: - EFO hospitalization: + description: >- + The admission and care of a patient in a hospital for + observation, diagnosis, or treatment. is_a: clinical intervention exact_mappings: - SNOMEDCT:32485007 @@ -9801,8 +10172,7 @@ classes: is_a: exposure event description: >- A pathological process, when viewed as an exposure, representing - a precondition, leading to or influencing an outcome, - e.g. autoimmunity leading to disease. + a precondition, leading to or influencing an outcome. pathological anatomical structure: description: >- @@ -9818,8 +10188,7 @@ classes: is_a: exposure event description: >- An abnormal anatomical structure, when viewed as an exposure, - representing an precondition, leading to or influencing an outcome, - e.g. thrombosis leading to an ischemic disease outcome. + represented as a precondition, leading to or influencing an outcome. disease or phenotypic feature exposure: is_a: exposure event @@ -9827,9 +10196,7 @@ classes: - pathological entity mixin description: >- A disease or phenotypic feature state, when viewed as an exposure, - represents an precondition, leading to or influencing an outcome, - e.g. HIV predisposing an individual to infections; a relative deficiency - of skin pigmentation predisposing an individual to skin cancer. + represented as a precondition, leading to or influencing an outcome,. chemical exposure: is_a: exposure event @@ -9849,7 +10216,7 @@ classes: is_a: exposure event description: >- A complex chemical exposure is an intake of a chemical - mixture (e.g. gasoline), other than a drug. + mixture, other than a drug. drug exposure: is_a: chemical exposure @@ -9937,7 +10304,7 @@ classes: is_a: exposure event description: >- A socioeconomic exposure is a factor relating to social and - financial status of an affected individual (e.g. poverty). + financial status of an affected individual. slot_usage: has attribute: range: socioeconomic attribute @@ -9950,7 +10317,7 @@ classes: description: >- An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible - biological or non-biological (e.g. clinical) outcomes. + biological or non-biological outcomes. pathological process outcome: mixins: @@ -10077,6 +10444,30 @@ classes: - OBAN:association - rdf:Statement - owl:Axiom + examples: + - object: + subject: NCBIGene:6910 # TBX5 + predicate: biolink:acts_upstream_of + object: GO:1901846 # positive regulation of cell communication by electrical coupling involved in cardiac conduction + category: biolink:Association + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["PMID:15289437"] + - object: + subject: NCBIGene:4357 # MPST + predicate: biolink:enables + object: GO:0005515 # protein binding + category: biolink:Association + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["PMID:32296183"] + - object: + subject: CHEBI:114566 # 2-imino-N,8-dimethyl-5-oxo-1-propan-2-yl-3-dipyrido[1,2-d:3',4'-f]pyrimidinecarboxamide + predicate: biolink:subclass_of + object: CHEBI:38166 # organic heteropolycyclic compound + category: biolink:Association + knowledge_level: knowledge_assertion + agent_type: manual_agent disease associated with response to chemical entity association: description: >- @@ -10280,9 +10671,9 @@ classes: - object slot_usage: subject: - range: gene - object: range: gene family + object: + range: gene or gene product predicate: subproperty_of: has part symmetric: false @@ -10547,9 +10938,32 @@ classes: object: range: chemical entity description: "the chemical element that is the target of the statement" + examples: + - object: + subject: CHEBI:85990 # panobinostat + predicate: biolink:has_metabolite + object: PUBCHEM.COMPOUND:155543741 # (E)-3-[4-[[2-(1a-methyl-2H-oxireno[2,3-b]indol-6b-yl)ethylamino]methyl]phenyl]-N-hydroxyprop-2-enamide + category: biolink:ChemicalEntityToChemicalEntityAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["PMID:22344701"] + species_context_qualifier: NCBITaxon:9606 + - object: + subject: CHEBI:85973 # edoxaban + predicate: biolink:has_metabolite + object: UNII:9O1PTP64VA + category: biolink:ChemicalEntityToChemicalEntityAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["PMID:22936313"] + species_context_qualifier: NCBITaxon:9606 reaction to participant association: - description: + description: >- + An association between a biochemical reaction and a participating + molecular entity, qualified by the stoichiometry, the side (reactant + vs. product) on which the participant appears, and the direction of + the reaction. is_a: chemical entity to chemical entity association slots: - stoichiometry @@ -10564,7 +10978,10 @@ classes: - object reaction to catalyst association: - description: + description: >- + A specialization of reaction-to-participant association in which the + participant is a gene or gene product (e.g., an enzyme) that catalyses + the reaction. is_a: reaction to participant association slot_usage: object: @@ -10620,6 +11037,49 @@ classes: object: range: disease or phenotypic feature description: "the disease or phenotype that is affected by the chemical" + examples: + - object: + subject: CHEBI:167638 # 2-hydroxy-5-{1-hydroxy-2-[(4-phenylbutan-2-yl)amino]ethyl}benzamide + predicate: biolink:contraindicated_in + object: UMLS:C0271149 # Secondary angle-closure glaucoma + category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation + knowledge_level: knowledge_assertion + agent_type: manual_validation_of_automated_agent + - object: + subject: CHEBI:25879 # pentaerythritol tetranitrate + predicate: biolink:contraindicated_in + object: UMLS:C0234976 # Lowered convulsive threshold + category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation + knowledge_level: knowledge_assertion + agent_type: manual_validation_of_automated_agent + - object: + subject: PUBCHEM.COMPOUND:134612761 # macimorelin + predicate: biolink:diagnoses + object: UMLS:C1720505 # Adult growth hormone deficiency + category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation + knowledge_level: knowledge_assertion + agent_type: manual_validation_of_automated_agent + - object: + subject: CHEBI:82720 # empagliflozin + predicate: biolink:preventative_for_condition + object: UMLS:C1320716 # Cardiovascular event + category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation + knowledge_level: knowledge_assertion + agent_type: manual_validation_of_automated_agent + - object: + subject: CHEBI:6919 # mezlocillin + predicate: biolink:treats + object: EFO:1001421 # Serratia Infections + category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation + knowledge_level: knowledge_assertion + agent_type: manual_validation_of_automated_agent + - object: + subject: CHEBI:135361 # methscopolamine + predicate: biolink:treats + object: MONDO:0005324 # seasonal allergic rhinitis + category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation + knowledge_level: knowledge_assertion + agent_type: manual_validation_of_automated_agent chemical or drug or treatment to disease or phenotypic feature association: description: >- @@ -10741,6 +11201,10 @@ classes: named thing associated with likelihood of named thing association: # TODO: better name description: >- + An association in which the subject entity is linked to the likelihood + of the object entity occurring, manifesting, or being observed. + Subject and object may each be qualified by aspect and context, and + the association may be further qualified by a population context. is_a: association slots: - subject @@ -10825,6 +11289,30 @@ classes: range: anatomical entity causal mechanism qualifier: range: CausalMechanismQualifierEnum + examples: + - object: + subject: CHEBI:135370 # aprindine + predicate: biolink:directly_physically_interacts_with + object: UniProtKB:P0DP23 # CALM1_HUMAN Calmodulin-1 (sprot) + category: biolink:ChemicalGeneInteractionAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + - object: + subject: CHEBI:4779 # emedastine + predicate: biolink:directly_physically_interacts_with + object: NCBIGene:3269 # HRH1 + category: biolink:ChemicalGeneInteractionAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["http://www.accessdata.fda.gov/drugsatfda_docs/label/2003/20706slr011_emadine_lbl.pdf"] + - object: + subject: UNII:OP35X9610Y # ACP-001 + predicate: biolink:interacts_with + object: NCBIGene:2690 # GHR + category: biolink:ChemicalGeneInteractionAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["https://www.accessdata.fda.gov/drugsatfda_docs/label/2021/761177Orig1s000lbl.pdf"] macromolecular machine has substrate association: is_a: association @@ -10841,6 +11329,21 @@ classes: subproperty_of: has substrate object: range: chemical entity or protein or polypeptide + examples: + - object: + subject: NCBIGene:6530 # SLC6A2 + predicate: biolink:has_substrate + object: CHEBI:5557 # guanethidine + category: biolink:MacromolecularMachineHasSubstrateAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + - object: + subject: NCBIGene:50719 # Slc7a5 + predicate: biolink:has_substrate + object: UNII:UID84303EL # borofalan (10B) + category: biolink:MacromolecularMachineHasSubstrateAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent gene regulates gene association: is_a: association @@ -10853,10 +11356,11 @@ classes: - species context qualifier slot_usage: subject: - range: gene or gene product - predicate: regulates + range: chemical entity or gene or gene product + predicate: + subproperty_of: regulates object: - range: gene or gene product + range: chemical entity or gene or gene product object aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum required: true @@ -10871,10 +11375,10 @@ classes: required: true examples: value: - subject: "NCBIGene:551" + subject: "NCBIGene:551" # AVP predicate: regulates qualified_predicate: causes - object: "NCBIGene:1636" + object: "NCBIGene:1636" # ACE object_aspect_qualifier: activity_or_abundance object_direction_qualifier: downregulated @@ -10959,19 +11463,86 @@ classes: - dgidb evidence score - evidence count - supporting documents + examples: + - object: + subject: PUBCHEM.COMPOUND:168290237 # 1-[4-(4-ethoxyphenyl)-4-(2H-tetrazol-5-yl)piperidin-1-yl]prop-2-en-1-one + predicate: biolink:affects + object: NCBIGene:200424 # TET3 + category: biolink:ChemicalAffectsGeneAssociation + knowledge_level: knowledge_assertion + agent_type: automated_agent + publications: ["PMID:35978680"] + object_aspect_qualifier: activity + object_direction_qualifier: decreased + causal_mechanism_qualifier: inhibition + qualified_predicate: biolink:causes + species_context_qualifier: NCBITaxon:9606 + - object: + subject: CHEBI:91447 # 4-methyl-3-[[1-methyl-6-(3-pyridinyl)-4-pyrazolo[3,4-d]pyrimidinyl]amino]-N-[3-(trifluoromethyl)phenyl]benzamide + predicate: biolink:directly_physically_interacts_with + object: NCBIGene:3313 # HSPA9 + category: biolink:ChemicalAffectsGeneAssociation + knowledge_level: knowledge_assertion + agent_type: automated_agent + publications: ["PMID:29928781"] + causal_mechanism_qualifier: binding + species_context_qualifier: NCBITaxon:9606 + - object: + subject: UNII:5V9KLZ54CY # Vinblastine + predicate: biolink:has_substrate + object: NCBIGene:5244 # ABCB4 + category: biolink:ChemicalAffectsGeneAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["PMID:20190787"] + species_context_qualifier: NCBITaxon:9606 + - object: + subject: CHEMBL.COMPOUND:CHEMBL1743027 # GIRENTUXIMAB + predicate: biolink:interacts_with + object: NCBIGene:768 # CA9 + category: biolink:ChemicalAffectsGeneAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["http://www.wilex.de/portfolio-english/rencarex/therapeutic-target/", "PMID:11941456"] + species_context_qualifier: NCBITaxon:9606 + - object: + subject: CHEBI:3546 # cepharanthine + predicate: biolink:affects + object: NCBIGene:4790 # NFKB1 + category: biolink:ChemicalAffectsGeneAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + object_aspect_qualifier: activity + object_direction_qualifier: decreased + causal_mechanism_qualifier: inhibition + qualified_predicate: biolink:causes gene affects chemical association: description: >- Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.) examples: - value: - subject: TRPC4 - predicate: affects - qualified_predicate: causes - object: Barium - object_aspect_qualifier: transport - object_direction_qualifier: increased + - object: + subject: NCBIGene:6616 # SNAP25 + predicate: biolink:affects + object: CHEMBL.COMPOUND:CHEMBL3707322 # LETIBOTULINUMTOXINA + category: biolink:GeneAffectsChemicalAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["CHEMBL.DOCUMENT:CHEMBL2107839", "https://www.accessdata.fda.gov/drugsatfda_docs/label/2024/761225s000lbl.pdf"] + subject_aspect_qualifier: hydrolysis + subject_direction_qualifier: increased + qualified_predicate: biolink:causes + species_context_qualifier: NCBITaxon:9606 + - object: + subject: CHEBI:3172 # bretylium + predicate: biolink:has_substrate + object: NCBIGene:6530 # SLC6A2 + category: biolink:GeneAffectsChemicalAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["ISBN:9780702034718 PP. 190-191", "PMID:18071295", "PMID:9142404"] + species_context_qualifier: NCBITaxon:9606 is_a: association slots: - subject form or variant qualifier @@ -10992,7 +11563,7 @@ classes: - species context qualifier slot_usage: subject: - range: gene or gene product + range: chemical entity or gene or gene product subject form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum subject part qualifier: @@ -11099,6 +11670,9 @@ classes: - object disease to entity association mixin: + description: >- + A mixin applied to any association whose subject (source node) + is a disease. mixin: true slots: - subject @@ -11228,6 +11802,9 @@ classes: - qualified predicate entity to phenotypic feature association mixin: + description: >- + A mixin applied to any association whose object (target node) + is a phenotypic feature. mixin: true is_a: entity to feature or disease qualifiers mixin mixins: @@ -11254,6 +11831,9 @@ classes: description: abnormal circulating bilirubin level phenotypic feature to entity association mixin: + description: >- + A mixin applied to any association whose subject (source node) + is a phenotypic feature. mixin: true is_a: feature or disease qualifiers to entity mixin mixins: @@ -11588,6 +12168,10 @@ classes: description: "chr13:g.32921033G>C (hg19) in ClinGen" gene to phenotypic feature association: + description: >- + An association between a gene or gene product and a phenotypic + feature, where variation in the gene is correlated with the + phenotypic feature. is_a: association slots: - subject form or variant qualifier @@ -11628,6 +12212,24 @@ classes: - if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children. gene to disease association: + description: >- + An association between a gene or gene product and a disease, + where variation in the gene is correlated with the disease. + examples: + - object: + subject: NCBIGene:60 # ACTB + predicate: biolink:associated_with + object: MONDO:0017579 # Baraitser-Winter cerebrofrontofacial syndrome + category: biolink:GeneToDiseaseAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + - object: + subject: UniProtKB:P11274-1 # breakpoint cluster region protein isoform h1 (human) + predicate: biolink:associated_with + object: MONDO:0011996 # chronic myelogenous leukemia, BCR-ABL1 positive + category: biolink:GeneToDiseaseAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent is_a: association exact_mappings: - SIO:000983 @@ -11666,6 +12268,9 @@ classes: - if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children. causal gene to disease association: + description: >- + An association between a gene and a disease where variation + in the gene has been shown to have a causal role in the disease. is_a: association defining_slots: - subject @@ -11687,6 +12292,12 @@ classes: range: disease correlated gene to disease association: + description: >- + An association between a gene (or gene product) and a disease for which + the gene is statistically correlated with the disease rather than + asserted as causal. Such associations typically derive from GWAS, + co-occurrence analyses, or other statistical methods, and are annotated + with scores such as a z-score or a diseases confidence score. is_a: association defining_slots: - subject @@ -11712,8 +12323,27 @@ classes: range: disease predicate: subproperty_of: correlated with + examples: + - object: + subject: NCBIGene:8506 # CNTNAP1 + predicate: biolink:occurs_together_in_literature_with + object: MONDO:0004585 # polyhydramnios + category: biolink:CorrelatedGeneToDiseaseAssociation + knowledge_level: text_co_occurrence + agent_type: data_analysis_pipeline + - object: + subject: UniProtKB:Q2KHT3-1 # protein CLEC16A isoform h1 (human) + predicate: biolink:occurs_together_in_literature_with + object: MONDO:0005578 # arthritic joint disease + category: biolink:CorrelatedGeneToDiseaseAssociation + knowledge_level: text_co_occurrence + agent_type: data_analysis_pipeline druggable gene to disease association: + description: >- + An association between a gene (or gene product) and a disease in which + the gene is classified by its druggability (e.g., via the IDG/Pharos + target development-level tiers). is_a: gene to disease association slots: - druggable gene category @@ -11735,6 +12365,9 @@ classes: - gene to entity association mixin phenotypic feature to disease association: + description: >- + An association between a phenotypic feature (sign or symptom) and a disease, + where the phenotypic feature is a manifestation or clinical indicator of the disease. is_a: association slot_usage: predicate: @@ -11850,6 +12483,10 @@ classes: Derivation relationships can also be used variant to phenotypic feature association: + description: >- + An association between a sequence variant and a phenotypic feature, in + which the allele state of the variant is linked to the manifestation + of the phenotype. is_a: association defining_slots: - subject @@ -11865,6 +12502,9 @@ classes: associated in some way with the phenotype state variant to disease association: + description: >- + An association between a sequence variant and a disease, in which the + allele state of the variant is linked to the disease state. is_a: association comments: - TODO decide no how to model pathogenicity @@ -11894,6 +12534,10 @@ classes: description: hereditary breast cancer genotype to disease association: + description: >- + An association between a genotype and a disease, in which the genotype + (typically a combination of alleles at one or more loci) is linked to + the disease state. is_a: association comments: - TODO decide no how to model pathogenicity @@ -11941,6 +12585,10 @@ classes: The relationship to the disease gene as a model of disease association: + description: >- + An association in which a gene (e.g., a model-organism ortholog of a + known disease gene) serves as a model of a human disease - for example, + because mutants of the gene recapitulate core features of the disease. is_a: gene to disease association defining_slots: - subject @@ -11958,6 +12606,10 @@ classes: mutants recapitulate core features of the disease. variant as a model of disease association: + description: >- + An association in which a sequence variant serves as a model of a + disease, recapitulating features relevant for studying the disease + outside of a patient who carries it. is_a: variant to disease association defining_slots: - subject @@ -11973,6 +12625,10 @@ classes: A variant that has a role in modeling the disease. genotype as a model of disease association: + description: >- + An association in which a genotype serves as a model of a disease, + recapitulating features relevant for studying the disease outside of + a patient who carries it. is_a: genotype to disease association defining_slots: - subject @@ -11988,6 +12644,10 @@ classes: A genotype that has a role in modeling the disease. cell line as a model of disease association: + description: >- + An association in which a cell line - typically derived from an + organismal entity with a disease state - serves as a model for that + disease in experimental settings. is_a: cell line to disease or phenotypic feature association defining_slots: - subject @@ -12004,6 +12664,11 @@ classes: as a model of that disease. organismal entity as a model of disease association: + description: >- + An association in which an organismal entity (e.g., a strain or breed) + serves as a model of a disease, either because it has a natural + predisposition to the disease or was bred or engineered specifically + to recapitulate it. is_a: association defining_slots: - subject @@ -12020,6 +12685,9 @@ classes: specifically to model a disease. organism to organism association: + description: >- + An association between two individual organisms (e.g., symbiosis, + parasitism, predation, or other inter-organism relationships). is_a: association defining_slots: - subject @@ -12034,6 +12702,10 @@ classes: An association between two individual organisms. taxon to taxon association: + description: >- + An association between two organism taxa, capturing ecological or + evolutionary relationships between the taxa (e.g., a host-pathogen + relationship or shared habitat). is_a: association defining_slots: - subject @@ -12048,6 +12720,11 @@ classes: An association between individuals of different taxa. gene has variant that contributes to disease association: + description: >- + A gene-to-disease association that is asserted on the grounds that the + gene harbours a sequence variant that contributes to the disease. + Qualifies the gene with the form or variant that underlies the + contribution. is_a: gene to disease association defining_slots: - subject @@ -12231,6 +12908,11 @@ classes: gene to go term association: + description: >- + A functional association between a gene (or gene product or + macromolecular complex) and a Gene Ontology (GO) term describing the + molecular function, biological process, or cellular component in which + it participates. aliases: ['functional association'] is_a: functional association exact_mappings: @@ -12257,8 +12939,78 @@ classes: examples: - value: GO:0016301 description: kinase activity + examples: + - object: + subject: NCBIGene:25595 # Map2 + predicate: biolink:active_in + object: GO:0015630 # microtubule cytoskeleton + category: biolink:GeneToGoTermAssociation + knowledge_level: prediction + agent_type: manual_validation_of_automated_agent + - object: + subject: NCBIGene:20502 # Slc16a2 + predicate: biolink:acts_upstream_of + object: GO:0042403 # thyroid hormone metabolic process + category: biolink:GeneToGoTermAssociation + knowledge_level: prediction + agent_type: manual_validation_of_automated_agent + - object: + subject: NCBIGene:308911 # Rrp8 + predicate: biolink:acts_upstream_of_negative_effect + object: GO:1903450 # regulation of G1 to G0 transition + category: biolink:GeneToGoTermAssociation + knowledge_level: prediction + agent_type: manual_validation_of_automated_agent + - object: + subject: NCBIGene:101148 # Samtor + predicate: biolink:acts_upstream_of_or_within + object: GO:0031669 # cellular response to nutrient levels + category: biolink:GeneToGoTermAssociation + knowledge_level: prediction + agent_type: manual_validation_of_automated_agent + - object: + subject: NCBIGene:18072 # Nhlh2 + predicate: biolink:acts_upstream_of_or_within_positive_effect + object: GO:0006915 # apoptotic process + category: biolink:GeneToGoTermAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + publications: ["PMID:17573818"] + - object: + subject: NCBIGene:12168 # Bmpr2 + predicate: biolink:colocalizes_with + object: GO:0005901 # caveola + category: biolink:GeneToGoTermAssociation + knowledge_level: prediction + agent_type: automated_agent + - object: + subject: NCBIGene:303888 # Osbpl11 + predicate: biolink:contributes_to + object: GO:0160270 # phosphatidylserine-phosphatidylinositol-4-phosphate exchange activity + category: biolink:GeneToGoTermAssociation + knowledge_level: prediction + agent_type: manual_validation_of_automated_agent + - object: + subject: NCBIGene:12193 # Zfp36l2 + predicate: biolink:enables + object: GO:0046872 # metal ion binding + category: biolink:GeneToGoTermAssociation + knowledge_level: prediction + agent_type: automated_agent + - object: + subject: NCBIGene:258177 # Or4c117 + predicate: biolink:located_in + object: GO:0016020 # membrane + category: biolink:GeneToGoTermAssociation + knowledge_level: prediction + agent_type: automated_agent + publications: ["PMID:14611657"] entity to disease association: + description: >- + An association between any entity and a disease, capturing + clinical context such as approval status, research phase, + FDA regulatory approvals, and number of cases. is_a: association exact_mappings: slots: @@ -12269,8 +13021,42 @@ classes: defining_slots: - subject - object + examples: + - object: + subject: CHEBI:50681 # methotrexate(2-) + predicate: biolink:in_clinical_trials_for + object: MONDO:0971091 # acute megakaryoblastic leukemia in adult + category: biolink:EntityToDiseaseAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + - object: + subject: CHEBI:9150 # simvastatin + predicate: biolink:treats + object: UMLS:C0520863 # Diastolic dysfunction + category: biolink:EntityToDiseaseAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + - object: + subject: CHEBI:28077 # rifampicin + predicate: biolink:applied_to_treat + object: MONDO:0005011 # Crohn disease + category: biolink:EntityToDiseaseAssociation + knowledge_level: observation + agent_type: manual_validation_of_automated_agent + - object: + subject: RXCUI:1367436 # 21 DAY ethinyl estradiol 0.000625 MG/HR / etonogestrel 0.005 MG/HR Vaginal System + predicate: biolink:contraindicated_in + object: MONDO:0004981 # atrial fibrillation + category: biolink:EntityToDiseaseAssociation + knowledge_level: knowledge_assertion + agent_type: manual_validation_of_automated_agent + publications: ["a280f164-2833-4f37-96e3-a857c91f77f2"] entity to phenotypic feature association: + description: >- + An association between any entity and a phenotypic feature, + capturing clinical context such as approval status, research phase, + FDA regulatory approvals, and number of cases. is_a: association exact_mappings: slots: @@ -12281,6 +13067,36 @@ classes: defining_slots: - subject - object + examples: + - object: + subject: GTOPDB:13663 # ponsegromab + predicate: biolink:in_clinical_trials_for + object: NCIT:C146753 # Fatigue, CTCAE 5.0 + category: biolink:EntityToPhenotypicFeatureAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + - object: + subject: CHEBI:6339 # etoricoxib + predicate: biolink:treats + object: HP:0001822 # Hallux valgus + category: biolink:EntityToPhenotypicFeatureAssociation + knowledge_level: knowledge_assertion + agent_type: manual_agent + - object: + subject: CHEBI:78538 # tafamidis + predicate: biolink:applied_to_treat + object: MONDO:0005294 # peripheral vascular disease + category: biolink:EntityToPhenotypicFeatureAssociation + knowledge_level: observation + agent_type: manual_validation_of_automated_agent + - object: + subject: RXCUI:617430 # amoxicillin 80 MG/ML / clavulanate 11.4 MG/ML Oral Suspension + predicate: biolink:contraindicated_in + object: HP:0001410 # Decreased liver function + category: biolink:EntityToPhenotypicFeatureAssociation + knowledge_level: knowledge_assertion + agent_type: manual_validation_of_automated_agent + publications: ["2970fe7e-9e1f-47aa-85ad-663ee15c7e06", "a5fa252a-d39e-4099-a230-b665fbb97a80", "b897c800-24a2-4e76-8668-498c5515c3d0", "babf3b8d-f2ce-407d-9407-728c45eb19ee", "d74e93e5-11c9-434e-a60c-4a4f911dd0f8"] ## ----------------- ## SEQUENCE FEATURES @@ -12395,6 +13211,9 @@ classes: anatomical entity to anatomical entity association: # schema: gocam + description: >- + An abstract parent class for associations between two anatomical entities, + such as part-of, develops-from, or other mereological and ontogenic relationships. is_a: association abstract: true defining_slots: @@ -12584,6 +13403,10 @@ classes: the environment in which the two taxa interact organism taxon to environment association: + description: >- + An abstract association between an organism taxon and an environmental + context (e.g., a habitat, biome, or ecological setting) in which the + taxon occurs. is_a: association abstract: true mixins: @@ -12684,6 +13507,11 @@ enums: ApprovalStatusEnum: description: >- + An enumeration of regulatory and development milestones for a drug or + therapeutic, spanning discovery, preclinical research, FDA clinical trial + phases (1-4), special review designations (e.g., fast track, breakthrough + therapy, priority review), regular FDA approval, and post-approval + withdrawal. permissible_values: "discovery_and_development_phase": description: >- @@ -12774,7 +13602,10 @@ enums: "post_approval_withdrawal": ClinicalApprovalStatusEnum: - description: + description: >- + An enumeration describing whether a chemical or therapy is approved for + use in treating a specific condition (e.g., FDA-approved for a condition, + not approved, off-label use, or withdrawn following approval). permissible_values: approved_for_condition: fda_approved_for_condition: @@ -12787,6 +13618,11 @@ enums: not_provided: ResearchPhaseEnum: + description: >- + An enumeration of research phases describing the stage of investigation + for a drug or therapy, spanning preclinical research through clinical + trial phases 1 through 4 (including phase 1/2 and phase 2/3 + combinations). permissible_values: pre_clinical_research_phase: description: >- @@ -12855,6 +13691,11 @@ enums: not_provided: DirectionQualifierEnum: + description: >- + An enumeration of values that qualify a change or effect by its + direction, i.e., whether the referenced quantity or activity is + increased (including up-regulated) or decreased (including + down-regulated). permissible_values: increased: upregulated: @@ -12879,10 +13720,19 @@ enums: - RO:0004033 ChemicalEntityDerivativeEnum: + description: >- + An enumeration of relationships by which one chemical entity is derived + from another, e.g., a metabolite produced from a parent compound. permissible_values: metabolite: ChemicalOrGeneOrGeneProductFormOrVariantEnum: + description: >- + An enumeration used as a qualifier to indicate a specific form or variant + of a chemical, gene, or gene product involved in an association (e.g., + modified form, loss-of-function variant, gain-of-function variant, + dominant-negative variant, polymorphic form, SNP form, mutant form, or + analog form). permissible_values: genetic_variant_form: is_a: modified_form @@ -12905,6 +13755,10 @@ enums: is_a: modified_form GeneOrGeneProductOrChemicalPartQualifierEnum: + description: >- + An enumeration used as a qualifier to indicate a particular structural or + functional part of a gene, gene product, or chemical (e.g., 3' UTR, 5' + UTR, poly-A tail, promoter, enhancer, exon, or intron). permissible_values: 3_prime_utr: 5_prime_utr: @@ -12915,6 +13769,14 @@ enums: intron: GeneOrGeneProductOrChemicalEntityAspectEnum: + description: >- + An enumeration used as a qualifier to indicate the specific aspect of a + gene, gene product, or chemical entity that is affected or measured in + an association. Values cover activity and abundance (expression, + synthesis, degradation, stability, localization, transport), molecular + interactions, and a wide range of molecular modifications such as + phosphorylation, methylation, acetylation, ubiquitination, and other + post-translational or chemical modifications. permissible_values: activity_or_abundance: description: >- @@ -13018,6 +13880,11 @@ enums: is_a: molecular_modification CausalMechanismQualifierEnum: + description: >- + An enumeration used as a qualifier to specify the causal or pharmacologic + mechanism by which an effect is exerted in an association (e.g., + agonism, antagonism, inverse agonism, allosteric modulation, + activation, inhibition, and their competitive or partial variants). permissible_values: modulation: description: >- @@ -13478,6 +14345,11 @@ enums: is_a: molecular_modification LogicalInterpretationEnum: + description: >- + An enumeration of logical interpretations that can be applied to a triple + to indicate whether the relation should be read as existential on both + sides (some-some), universal-existential (all-some), or its inverse + (inverse all-some). permissible_values: some_some: description: >- @@ -13490,6 +14362,10 @@ enums: inverse_all_some: ReactionDirectionEnum: + description: >- + An enumeration of possible directions for a biochemical reaction, + indicating whether it proceeds left-to-right, right-to-left, is + bidirectional (reversible), or has no net direction. permissible_values: left_to_right: right_to_left: @@ -13497,6 +14373,10 @@ enums: neutral: ReactionSideEnum: + description: >- + An enumeration indicating on which side of a biochemical reaction a + participant appears - the left-hand (reactant/substrate) side or the + right-hand (product) side, as written. permissible_values: left: right: @@ -13529,6 +14409,12 @@ enums: description: amino acid DruggableGeneCategoryEnum: + description: >- + An enumeration of druggability categories for gene targets as defined by + the IDG (Illuminating the Druggable Genome) / Pharos target development + level classification: Tclin (targets of approved drugs), Tchem (targets + with potent bioactives), Tbio (targets with biological knowledge), and + Tdark (poorly characterized targets). permissible_values: "tclin": description: >- @@ -13553,6 +14439,9 @@ enums: DrugAvailabilityEnum: description: >- + An enumeration describing how a drug or chemical entity may be obtained, + distinguishing products that are available over the counter from those + that require a prescription. permissible_values: "over_the_counter": description: >- @@ -13562,6 +14451,10 @@ enums: chemical entity is available by prescription. DrugDeliveryEnum: + description: >- + An enumeration of routes by which a drug is administered or delivered to + a patient, including inhalation, oral, transdermal absorption, and + various forms of injection (intravenous, subcutaneous, intramuscular). permissible_values: inhalation: oral: @@ -13668,6 +14561,13 @@ enums: - translator_minimal AgentTypeEnum: + description: >- + An enumeration of agent types responsible for generating a statement of + knowledge, as defined by the Translator Knowledge Level / Agent Type + (KL/AT) standard. Values distinguish human (manual) agents from + automated agents (including data analysis pipelines, computational + models, text-mining agents, image-processing agents) and mixed cases + such as manual validation of automated output. permissible_values: manual_agent: description: >- @@ -13761,6 +14661,13 @@ enums: - translator_minimal KnowledgeLevelEnum: + description: >- + An enumeration characterizing the type of knowledge expressed in a + statement and the kind of evidence and reasoning that supports it, as + defined by the Translator Knowledge Level / Agent Type (KL/AT) + standard. Values include knowledge assertion, logical entailment, + prediction, statistical association, text co-occurrence, direct + observation, and not-provided. permissible_values: knowledge_assertion: aliases: ['assertion'] diff --git a/config.yaml b/config.yaml index 56da66d8c..026127fbe 100644 --- a/config.yaml +++ b/config.yaml @@ -11,8 +11,6 @@ generator_args: # metadata_profile: rdfs markdown: mergeimports: true - graphql: - mergeimports: true java: mergeimports: true metadata: true @@ -20,6 +18,7 @@ generator_args: mergeimports: true jsonschema: mergeimports: true + include_range_class_descendants: true jsonldcontext: mergeimports: true python: diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql index ee76ca044..1670d73df 100644 --- a/project/graphql/biolink_model.graphql +++ b/project/graphql/biolink_model.graphql @@ -431,13 +431,13 @@ type AccessibleDnaRegion implements GenomicEntity, ChemicalEntityOrGeneOrGenePro hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasBiologicalSequence: BiologicalSequence @@ -453,13 +453,13 @@ type Activity implements ActivityAndBehavior hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } interface ActivityAndBehavior @@ -476,13 +476,13 @@ interface AdministrativeEntity hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type AffinityMeasurement @@ -495,13 +495,13 @@ type AffinityMeasurement hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! affinityParameter: AffinityParameterEnum affinity: Float hasBinaryRelation: BinaryRelationEnum @@ -515,14 +515,14 @@ type Agent hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! - affiliation: [Uriorcurie] + taxon: String + category: [String]! + affiliation: [String] address: String id: String! name: LabelType @@ -537,13 +537,13 @@ type AnatomicalEntity implements PhysicalEssence, OntologyClass description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -571,7 +571,7 @@ type AnatomicalEntityHasPartAnatomicalEntityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -590,16 +590,16 @@ type AnatomicalEntityHasPartAnatomicalEntityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: AnatomicalEntity! object: AnatomicalEntity! - predicate: Uriorcurie! + predicate: String! } type AnatomicalEntityPartOfAnatomicalEntityAssociation @@ -624,7 +624,7 @@ type AnatomicalEntityPartOfAnatomicalEntityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -643,16 +643,16 @@ type AnatomicalEntityPartOfAnatomicalEntityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: AnatomicalEntity! object: AnatomicalEntity! - predicate: Uriorcurie! + predicate: String! } interface AnatomicalEntityToAnatomicalEntityAssociation @@ -663,7 +663,7 @@ interface AnatomicalEntityToAnatomicalEntityAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -678,7 +678,7 @@ interface AnatomicalEntityToAnatomicalEntityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -697,13 +697,13 @@ interface AnatomicalEntityToAnatomicalEntityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: AnatomicalEntity! object: AnatomicalEntity! } @@ -730,7 +730,7 @@ type AnatomicalEntityToAnatomicalEntityOntogenicAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -749,16 +749,16 @@ type AnatomicalEntityToAnatomicalEntityOntogenicAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: AnatomicalEntity! object: AnatomicalEntity! - predicate: Uriorcurie! + predicate: String! } interface Annotation @@ -775,24 +775,24 @@ type Article providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String authors: [Agent] pages: [String] summary: String keywords: [String] - meshTerms: [Uriorcurie] - xref: [Uriorcurie] + meshTerms: [String] + xref: [String] publicationType: [String]! id: String! name: LabelType - publishedIn: Uriorcurie! + publishedIn: String! isoAbbreviation: String volume: String issue: String @@ -807,7 +807,7 @@ type Association hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -823,7 +823,7 @@ type Association agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -842,13 +842,13 @@ type Association adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] } type Attribute implements OntologyClass @@ -859,13 +859,13 @@ type Attribute implements OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -882,13 +882,13 @@ type Bacterium description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -904,13 +904,13 @@ type Behavior implements OntologyClass, ActivityAndBehavior hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasInput: [NamedThing] @@ -926,7 +926,7 @@ type BehaviorToBehavioralFeatureAssociation implements EntityToPhenotypicFeature description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -941,7 +941,7 @@ type BehaviorToBehavioralFeatureAssociation implements EntityToPhenotypicFeature agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -960,13 +960,13 @@ type BehaviorToBehavioralFeatureAssociation implements EntityToPhenotypicFeature adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: Behavior! object: BehavioralFeature! frequencyQualifier: FrequencyValue @@ -974,13 +974,13 @@ type BehaviorToBehavioralFeatureAssociation implements EntityToPhenotypicFeature subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease sexQualifier: BiologicalSex - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float } type BehavioralExposure @@ -992,20 +992,20 @@ type BehavioralExposure hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -1021,13 +1021,13 @@ type BehavioralFeature hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType inheritance: GeneticInheritance @@ -1047,13 +1047,13 @@ type BiologicalEntity implements ThingWithTaxon hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -1068,13 +1068,13 @@ type BiologicalProcess implements Occurrent, OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasInput: [NamedThing] @@ -1092,13 +1092,13 @@ type BiologicalProcessOrActivity implements Occurrent, OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasInput: [NamedThing] @@ -1114,7 +1114,7 @@ type BiologicalProcessOrActivityToAnatomicalEntityAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -1129,7 +1129,7 @@ type BiologicalProcessOrActivityToAnatomicalEntityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1148,13 +1148,13 @@ type BiologicalProcessOrActivityToAnatomicalEntityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: BiologicalProcessOrActivity! object: AnatomicalEntity! } @@ -1181,7 +1181,7 @@ type BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1200,16 +1200,16 @@ type BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: BiologicalProcessOrActivity! object: BiologicalProcessOrActivity! - predicate: Uriorcurie! + predicate: String! } type BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation @@ -1234,7 +1234,7 @@ type BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1253,16 +1253,16 @@ type BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: BiologicalProcessOrActivity! object: GeneOrGeneProductOrGeneFamily! - predicate: Uriorcurie! + predicate: String! } type BiologicalSex @@ -1273,13 +1273,13 @@ type BiologicalSex hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -1296,20 +1296,20 @@ type BioticExposure hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -1324,20 +1324,20 @@ type Book providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String authors: [Agent] pages: [String] summary: String keywords: [String] - meshTerms: [Uriorcurie] - xref: [Uriorcurie] + meshTerms: [String] + xref: [String] publicationType: [String]! name: LabelType id: String! @@ -1354,24 +1354,24 @@ type BookChapter providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String authors: [Agent] pages: [String] summary: String keywords: [String] - meshTerms: [Uriorcurie] - xref: [Uriorcurie] + meshTerms: [String] + xref: [String] publicationType: [String]! id: String! name: LabelType - publishedIn: Uriorcurie! + publishedIn: String! volume: String chapter: String } @@ -1385,13 +1385,13 @@ type Case implements SubjectOfInvestigation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -1420,7 +1420,7 @@ type CaseToDiseaseAssociation implements CaseToEntityAssociationMixin agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1439,15 +1439,15 @@ type CaseToDiseaseAssociation implements CaseToEntityAssociationMixin adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: Disease! onsetQualifier: Onset } @@ -1455,7 +1455,7 @@ type CaseToDiseaseAssociation implements CaseToEntityAssociationMixin interface CaseToEntityAssociationMixin { subject: Case! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -1481,7 +1481,7 @@ type CaseToGeneAssociation implements CaseToEntityAssociationMixin agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1500,15 +1500,15 @@ type CaseToGeneAssociation implements CaseToEntityAssociationMixin adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: GeneOrGeneProduct! } @@ -1521,7 +1521,7 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! qualifier: String qualifiers: [OntologyClass] @@ -1536,7 +1536,7 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1555,13 +1555,13 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] negated: Boolean onsetQualifier: Onset frequencyQualifier: FrequencyValue @@ -1569,13 +1569,13 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease sexQualifier: BiologicalSex - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float } type CaseToVariantAssociation implements CaseToEntityAssociationMixin @@ -1600,7 +1600,7 @@ type CaseToVariantAssociation implements CaseToEntityAssociationMixin agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1619,15 +1619,15 @@ type CaseToVariantAssociation implements CaseToEntityAssociationMixin adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: SequenceVariant! hasZygosity: Zygosity } @@ -1640,7 +1640,7 @@ type CausalGeneToDiseaseAssociation implements GeneToEntityAssociationMixin description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -1655,7 +1655,7 @@ type CausalGeneToDiseaseAssociation implements GeneToEntityAssociationMixin agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1674,18 +1674,18 @@ type CausalGeneToDiseaseAssociation implements GeneToEntityAssociationMixin adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subjectFormOrVariantQualifier: String subjectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum allelicRequirement: String - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String subject: GeneOrGeneProduct! object: Disease! } @@ -1699,13 +1699,13 @@ type Cell description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -1720,13 +1720,13 @@ type CellLine implements SubjectOfInvestigation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -1740,7 +1740,7 @@ type CellLineAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -1756,7 +1756,7 @@ type CellLineAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1775,16 +1775,16 @@ type CellLineAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] diseaseContextQualifier: Disease - subjectSpecializationQualifier: Uriorcurie - objectSpecializationQualifier: Uriorcurie + subjectSpecializationQualifier: String + objectSpecializationQualifier: String anatomicalContextQualifier: [String] subject: CellLine! frequencyQualifier: FrequencyValue @@ -1792,7 +1792,7 @@ type CellLineAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String } type CellLineToDiseaseOrPhenotypicFeatureAssociation implements CellLineToEntityAssociationMixin, EntityToDiseaseOrPhenotypicFeatureAssociationMixin @@ -1803,7 +1803,7 @@ type CellLineToDiseaseOrPhenotypicFeatureAssociation implements CellLineToEntity description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -1819,7 +1819,7 @@ type CellLineToDiseaseOrPhenotypicFeatureAssociation implements CellLineToEntity agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1838,24 +1838,24 @@ type CellLineToDiseaseOrPhenotypicFeatureAssociation implements CellLineToEntity adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: DiseaseOrPhenotypicFeature! diseaseContextQualifier: Disease - subjectSpecializationQualifier: Uriorcurie - objectSpecializationQualifier: Uriorcurie + subjectSpecializationQualifier: String + objectSpecializationQualifier: String anatomicalContextQualifier: [String] } interface CellLineToEntityAssociationMixin { subject: CellLine! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -1868,13 +1868,13 @@ type CellularComponent description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -1889,13 +1889,13 @@ type CellularOrganism implements SubjectOfInvestigation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -1923,7 +1923,7 @@ type ChemicalAffectsBiologicalEntityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -1942,13 +1942,13 @@ type ChemicalAffectsBiologicalEntityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subjectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum subjectPartQualifier: GeneOrGeneProductOrChemicalPartQualifierEnum subjectDerivativeQualifier: ChemicalEntityDerivativeEnum @@ -1962,10 +1962,10 @@ type ChemicalAffectsBiologicalEntityAssociation objectDirectionQualifier: DirectionQualifierEnum causalMechanismQualifier: CausalMechanismQualifierEnum anatomicalContextQualifier: [AnatomicalEntity] - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String speciesContextQualifier: OrganismTaxon subject: ChemicalEntity! - predicate: Uriorcurie! + predicate: String! object: BiologicalEntity! } @@ -1991,7 +1991,7 @@ type ChemicalAffectsGeneAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2010,12 +2010,12 @@ type ChemicalAffectsGeneAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - semmedAgreementCount: Integer + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subjectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum subjectPartQualifier: GeneOrGeneProductOrChemicalPartQualifierEnum subjectDerivativeQualifier: ChemicalEntityDerivativeEnum @@ -2029,15 +2029,15 @@ type ChemicalAffectsGeneAssociation objectDirectionQualifier: DirectionQualifierEnum causalMechanismQualifier: CausalMechanismQualifierEnum anatomicalContextQualifier: [AnatomicalEntity] - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String speciesContextQualifier: OrganismTaxon subject: ChemicalEntity! - predicate: Uriorcurie! + predicate: String! object: BiologicalEntity! dgidbInteractionScore: Float - dgidbEvidenceScore: Integer - evidenceCount: Integer - supportingDocuments: [Uriorcurie] + dgidbEvidenceScore: Int + evidenceCount: Int + supportingDocuments: [String] } type ChemicalEntity implements PhysicalEssence, ChemicalOrDrugOrTreatment, ChemicalEntityOrGeneOrGeneProduct, ChemicalEntityOrProteinOrPolypeptide @@ -2050,13 +2050,13 @@ type ChemicalEntity implements PhysicalEssence, ChemicalOrDrugOrTreatment, Chemi hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -2093,7 +2093,7 @@ type ChemicalEntityAssessesNamedThingAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2112,16 +2112,16 @@ type ChemicalEntityAssessesNamedThingAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: ChemicalEntity! object: NamedThing! - predicate: Uriorcurie! + predicate: String! } interface ChemicalEntityOrGeneOrGeneProduct @@ -2150,7 +2150,7 @@ type ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2169,15 +2169,15 @@ type ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] objectDirectionQualifier: DirectionQualifierEnum - predicate: Uriorcurie! + predicate: String! subject: ChemicalEntityOrGeneOrGeneProduct! object: GeneOrGeneProduct! } @@ -2208,7 +2208,7 @@ type ChemicalEntityToBiologicalProcessAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2227,20 +2227,20 @@ type ChemicalEntityToBiologicalProcessAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] speciesContextQualifier: OrganismTaxon anatomicalContextQualifier: [String] - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String objectDirectionQualifier: DirectionQualifierEnum subject: ChemicalEntity! object: BiologicalProcess! - predicate: Uriorcurie! + predicate: String! } type ChemicalEntityToChemicalDerivationAssociation @@ -2265,7 +2265,7 @@ type ChemicalEntityToChemicalDerivationAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2284,18 +2284,18 @@ type ChemicalEntityToChemicalDerivationAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] speciesContextQualifier: OrganismTaxon catalystQualifier: [MacromolecularMachineMixin] subject: ChemicalEntity! object: ChemicalEntity! - predicate: Uriorcurie! + predicate: String! } type ChemicalEntityToChemicalEntityAssociation @@ -2320,7 +2320,7 @@ type ChemicalEntityToChemicalEntityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2339,15 +2339,15 @@ type ChemicalEntityToChemicalEntityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: ChemicalEntity! speciesContextQualifier: OrganismTaxon } @@ -2361,7 +2361,7 @@ type ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation implements EntityToDi hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -2376,7 +2376,7 @@ type ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation implements EntityToDi agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2395,26 +2395,26 @@ type ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation implements EntityToDi adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] clinicalApprovalStatus: ClinicalApprovalStatusEnum maxResearchPhase: ResearchPhaseEnum object: DiseaseOrPhenotypicFeature! diseaseContextQualifier: Disease - subjectSpecializationQualifier: Uriorcurie - objectSpecializationQualifier: Uriorcurie + subjectSpecializationQualifier: String + objectSpecializationQualifier: String anatomicalContextQualifier: [String] } interface ChemicalEntityToEntityAssociationMixin { subject: ChemicalEntityOrGeneOrGeneProduct! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -2426,7 +2426,7 @@ type ChemicalEntityToPathwayAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -2441,7 +2441,7 @@ type ChemicalEntityToPathwayAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2460,13 +2460,13 @@ type ChemicalEntityToPathwayAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: ChemicalEntity! object: Pathway! } @@ -2480,20 +2480,20 @@ type ChemicalExposure hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -2522,7 +2522,7 @@ type ChemicalGeneInteractionAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2541,19 +2541,19 @@ type ChemicalGeneInteractionAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] hasAffinity: [AffinityMeasurement] subjectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum subjectPartQualifier: GeneOrGeneProductOrChemicalPartQualifierEnum subjectDerivativeQualifier: ChemicalEntityDerivativeEnum subjectContextQualifier: AnatomicalEntity - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String objectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum objectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum @@ -2562,10 +2562,10 @@ type ChemicalGeneInteractionAssociation anatomicalContextQualifier: [AnatomicalEntity] causalMechanismQualifier: CausalMechanismQualifierEnum dgidbInteractionScore: Float - dgidbEvidenceScore: Integer + dgidbEvidenceScore: Int subject: ChemicalEntity! object: GeneOrGeneProduct! - predicate: Uriorcurie! + predicate: String! } type ChemicalMixture implements OntologyClass @@ -2578,13 +2578,13 @@ type ChemicalMixture implements OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -2630,7 +2630,7 @@ type ChemicalOrDrugOrTreatmentAdverseEventAssociation implements EntityToDisease agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2649,25 +2649,25 @@ type ChemicalOrDrugOrTreatmentAdverseEventAssociation implements EntityToDisease adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] fDAAdverseEventLevel: FDAIDAAdverseEventEnum - predicate: Uriorcurie! + predicate: String! diseaseContextQualifier: Disease - subjectSpecializationQualifier: Uriorcurie - objectSpecializationQualifier: Uriorcurie + subjectSpecializationQualifier: String + objectSpecializationQualifier: String anatomicalContextQualifier: [String] frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String } type ChemicalOrDrugOrTreatmentSideEffectAssociation implements EntityToDiseaseOrPhenotypicFeatureAssociationMixin, EntityToFeatureOrDiseaseQualifiersMixin @@ -2694,7 +2694,7 @@ type ChemicalOrDrugOrTreatmentSideEffectAssociation implements EntityToDiseaseOr agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2713,24 +2713,24 @@ type ChemicalOrDrugOrTreatmentSideEffectAssociation implements EntityToDiseaseOr adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! diseaseContextQualifier: Disease - subjectSpecializationQualifier: Uriorcurie - objectSpecializationQualifier: Uriorcurie + subjectSpecializationQualifier: String + objectSpecializationQualifier: String anatomicalContextQualifier: [String] frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String } type ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation implements EntityToDiseaseOrPhenotypicFeatureAssociationMixin, EntityToFeatureOrDiseaseQualifiersMixin @@ -2757,7 +2757,7 @@ type ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation implements agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -2776,24 +2776,24 @@ type ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation implements adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! diseaseContextQualifier: Disease - subjectSpecializationQualifier: Uriorcurie - objectSpecializationQualifier: Uriorcurie + subjectSpecializationQualifier: String + objectSpecializationQualifier: String anatomicalContextQualifier: [String] frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String } type ChemicalRole @@ -2804,13 +2804,13 @@ type ChemicalRole hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -2821,7 +2821,7 @@ type ChemicalRole interface ChemicalToEntityAssociationMixin { subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -2835,13 +2835,13 @@ type ChiSquaredAnalysisResult hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type ClinicalAttribute @@ -2852,13 +2852,13 @@ type ClinicalAttribute hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -2874,13 +2874,13 @@ type ClinicalCourse hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -2898,13 +2898,13 @@ type ClinicalEntity hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type ClinicalFinding @@ -2916,13 +2916,13 @@ type ClinicalFinding description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType inheritance: GeneticInheritance @@ -2939,13 +2939,13 @@ type ClinicalIntervention hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type ClinicalMeasurement @@ -2956,13 +2956,13 @@ type ClinicalMeasurement hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasQuantitativeValue: [QuantityValue] hasQualitativeValue: NamedThing @@ -2978,13 +2978,13 @@ type ClinicalModifier hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -3002,13 +3002,13 @@ type ClinicalTrial hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! hasStudyResults: [StudyResult] clinicalTrialPhase: ResearchPhaseEnum clinicalTrialPrimaryPurpose: String @@ -3017,13 +3017,13 @@ type ClinicalTrial clinicalTrialBriefTitle: String clinicalTrialEnrollmentType: String clinicalTrialStartDate: String - clinicalTrialEnrollment: Integer + clinicalTrialEnrollment: Int clinicalTrialAgeStage: [ClinicalTrialAgeStageEnum] clinicalTrialAgeRange: String clinicalTrialTestedIntervention: String clinicalTrialInterventions: [ClinicalIntervention] clinicalTrialConditions: [DiseaseOrPhenotypicFeature] - creationDate: Date + creationDate: String } type CodingSequence implements GenomicEntity @@ -3036,13 +3036,13 @@ type CodingSequence implements GenomicEntity hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasBiologicalSequence: BiologicalSequence @@ -3057,13 +3057,13 @@ type Cohort implements SubjectOfInvestigation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -3079,17 +3079,17 @@ type CommonDataElement hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String } type ComplexChemicalExposure @@ -3101,20 +3101,20 @@ type ComplexChemicalExposure hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -3130,13 +3130,13 @@ type ComplexMolecularMixture hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -3164,13 +3164,13 @@ type ConceptCountAnalysisResult hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type ConfidenceLevel @@ -3183,17 +3183,17 @@ type ConfidenceLevel hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String } type ContributorAssociation @@ -3217,7 +3217,7 @@ type ContributorAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -3236,15 +3236,15 @@ type ContributorAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: InformationContentEntity! - predicate: Uriorcurie! + predicate: String! object: Agent! qualifiers: [OntologyClass] } @@ -3271,7 +3271,7 @@ type CorrelatedGeneToDiseaseAssociation implements EntityToDiseaseAssociationMix agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -3290,23 +3290,23 @@ type CorrelatedGeneToDiseaseAssociation implements EntityToDiseaseAssociationMix adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] zScore: Float diseasesConfidenceScore: Float subjectFormOrVariantQualifier: String subjectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum allelicRequirement: String - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String subject: GeneOrGeneProduct! object: Disease! - predicate: Uriorcurie! + predicate: String! frequencyQualifier: FrequencyValue subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String @@ -3323,17 +3323,17 @@ type Dataset hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String } type DatasetDistribution @@ -3346,17 +3346,17 @@ type DatasetDistribution hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String distributionDownloadUrl: String } @@ -3370,17 +3370,17 @@ type DatasetSummary hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String sourceWebPage: String sourceLogo: String } @@ -3395,17 +3395,17 @@ type DatasetVersion hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String hasDataset: Dataset ingestDate: String hasDistribution: DatasetDistribution @@ -3421,13 +3421,13 @@ type Device hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type DiagnosticAid @@ -3440,13 +3440,13 @@ type DiagnosticAid hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type Disease @@ -3459,13 +3459,13 @@ type Disease hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType inheritance: GeneticInheritance @@ -3493,7 +3493,7 @@ type DiseaseAssociatedWithResponseToChemicalEntityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -3512,18 +3512,18 @@ type DiseaseAssociatedWithResponseToChemicalEntityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] responseContextQualifier: ResponseEnum responseTargetContextQualifier: ResponseTargetEnum subject: Disease! object: ChemicalEntity! - predicate: Uriorcurie! + predicate: String! } type DiseaseOrPhenotypicFeature implements OntologyClass @@ -3536,13 +3536,13 @@ type DiseaseOrPhenotypicFeature implements OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType inheritance: GeneticInheritance @@ -3557,20 +3557,20 @@ type DiseaseOrPhenotypicFeatureExposure implements PathologicalEntityMixin hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -3583,7 +3583,7 @@ type DiseaseOrPhenotypicFeatureOutcome implements Outcome interface DiseaseOrPhenotypicFeatureToEntityAssociationMixin { subject: DiseaseOrPhenotypicFeature! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -3610,7 +3610,7 @@ type DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation implements Diseas agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -3629,14 +3629,14 @@ type DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation implements Diseas adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! object: GeneticInheritance! } @@ -3649,7 +3649,7 @@ type DiseaseOrPhenotypicFeatureToLocationAssociation implements DiseaseOrPhenoty hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -3664,7 +3664,7 @@ type DiseaseOrPhenotypicFeatureToLocationAssociation implements DiseaseOrPhenoty agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -3683,20 +3683,20 @@ type DiseaseOrPhenotypicFeatureToLocationAssociation implements DiseaseOrPhenoty adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] object: AnatomicalEntity! } interface DiseaseToEntityAssociationMixin { subject: Disease! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -3709,7 +3709,7 @@ type DiseaseToExposureEventAssociation implements DiseaseToEntityAssociationMixi hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -3725,7 +3725,7 @@ type DiseaseToExposureEventAssociation implements DiseaseToEntityAssociationMixi agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -3744,13 +3744,13 @@ type DiseaseToExposureEventAssociation implements DiseaseToEntityAssociationMixi adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] } type DiseaseToPhenotypicFeatureAssociation implements FrequencyQuantifier, EntityToPhenotypicFeatureAssociationMixin, DiseaseToEntityAssociationMixin @@ -3761,7 +3761,7 @@ type DiseaseToPhenotypicFeatureAssociation implements FrequencyQuantifier, Entit description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -3776,7 +3776,7 @@ type DiseaseToPhenotypicFeatureAssociation implements FrequencyQuantifier, Entit agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -3795,26 +3795,26 @@ type DiseaseToPhenotypicFeatureAssociation implements FrequencyQuantifier, Entit adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] onsetQualifier: Onset subject: Disease! object: PhenotypicFeature! - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease sexQualifier: BiologicalSex } @@ -3829,13 +3829,13 @@ type Drug implements ChemicalOrDrugOrTreatment, OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -3862,20 +3862,20 @@ type DrugExposure hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -3892,20 +3892,20 @@ type DrugLabel providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String authors: [Agent] pages: [String] summary: String keywords: [String] - meshTerms: [Uriorcurie] - xref: [Uriorcurie] + meshTerms: [String] + xref: [String] publicationType: [String]! id: String! name: LabelType @@ -3914,7 +3914,7 @@ type DrugLabel interface DrugToEntityAssociationMixin { subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -3927,7 +3927,7 @@ type DrugToGeneAssociation implements DrugToEntityAssociationMixin hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -3942,7 +3942,7 @@ type DrugToGeneAssociation implements DrugToEntityAssociationMixin agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -3961,13 +3961,13 @@ type DrugToGeneAssociation implements DrugToEntityAssociationMixin adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] object: GeneOrGeneProduct! } @@ -3980,20 +3980,20 @@ type DrugToGeneInteractionExposure implements GeneGroupingMixin hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -4023,7 +4023,7 @@ type DruggableGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixi agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -4042,18 +4042,18 @@ type DruggableGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixi adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subjectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum objectDirectionQualifier: DirectionQualifierEnum allelicRequirement: String - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseasesConfidenceScore: Float gene2phenotypeConfidenceCategory: String object: Disease! @@ -4074,7 +4074,7 @@ interface Entity { id: String! iri: IriType - category: [Uriorcurie] + category: [String] type: [String] name: LabelType description: NarrativeText @@ -4091,7 +4091,7 @@ type EntityToDiseaseAssociation hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -4107,7 +4107,7 @@ type EntityToDiseaseAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -4126,29 +4126,29 @@ type EntityToDiseaseAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] clinicalApprovalStatus: ClinicalApprovalStatusEnum maxResearchPhase: ResearchPhaseEnum fDARegulatoryApprovals: [String] - numberOfCases: Integer + numberOfCases: Int } interface EntityToDiseaseAssociationMixin { frequencyQualifier: FrequencyValue subject: NamedThing! - predicate: Uriorcurie! + predicate: String! subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease object: Disease! } @@ -4156,18 +4156,18 @@ interface EntityToDiseaseAssociationMixin interface EntityToDiseaseOrPhenotypicFeatureAssociationMixin { subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: DiseaseOrPhenotypicFeature! diseaseContextQualifier: Disease - subjectSpecializationQualifier: Uriorcurie - objectSpecializationQualifier: Uriorcurie + subjectSpecializationQualifier: String + objectSpecializationQualifier: String anatomicalContextQualifier: [String] } interface EntityToExposureEventAssociationMixin { subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: ExposureEvent! } @@ -4175,13 +4175,13 @@ interface EntityToFeatureOrDiseaseQualifiersMixin { frequencyQualifier: FrequencyValue subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease } @@ -4189,32 +4189,32 @@ interface EntityToFeatureOrGeneQualifiersMixin { frequencyQualifier: FrequencyValue subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String } interface EntityToFeatureOrVariantQualifiersMixin { frequencyQualifier: FrequencyValue subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String } interface EntityToOutcomeAssociationMixin { subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: Outcome! } @@ -4227,7 +4227,7 @@ type EntityToPhenotypicFeatureAssociation hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -4243,7 +4243,7 @@ type EntityToPhenotypicFeatureAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -4262,17 +4262,17 @@ type EntityToPhenotypicFeatureAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] clinicalApprovalStatus: ClinicalApprovalStatusEnum maxResearchPhase: ResearchPhaseEnum fDARegulatoryApprovals: [String] - numberOfCases: Integer + numberOfCases: Int } type EntityToPhenotypicFeatureAssociationMixin implements FrequencyQuantifier @@ -4282,16 +4282,16 @@ type EntityToPhenotypicFeatureAssociationMixin implements FrequencyQuantifier subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: PhenotypicFeature! sexQualifier: BiologicalSex - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float } type EnvironmentalExposure @@ -4303,20 +4303,20 @@ type EnvironmentalExposure hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -4332,13 +4332,13 @@ type EnvironmentalFeature hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type EnvironmentalFoodContaminant @@ -4351,13 +4351,13 @@ type EnvironmentalFoodContaminant hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -4382,13 +4382,13 @@ type EnvironmentalProcess implements Occurrent hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type EpidemiologicalOutcome implements Outcome @@ -4410,13 +4410,13 @@ type Event hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type Evidence @@ -4429,17 +4429,17 @@ type Evidence hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String } type EvidenceType implements OntologyClass @@ -4452,13 +4452,13 @@ type EvidenceType implements OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type Exon @@ -4471,13 +4471,13 @@ type Exon hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -4490,7 +4490,7 @@ type ExonToTranscriptRelationship description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -4505,7 +4505,7 @@ type ExonToTranscriptRelationship agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -4524,13 +4524,13 @@ type ExonToTranscriptRelationship adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: Exon! object: Transcript! } @@ -4544,20 +4544,20 @@ type ExposureEvent implements OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -4572,7 +4572,7 @@ type ExposureEventToOutcomeAssociation implements EntityToOutcomeAssociationMixi hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -4588,7 +4588,7 @@ type ExposureEventToOutcomeAssociation implements EntityToOutcomeAssociationMixi agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -4607,13 +4607,13 @@ type ExposureEventToOutcomeAssociation implements EntityToOutcomeAssociationMixi adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] populationContextQualifier: PopulationOfIndividualOrganisms temporalContextQualifier: TimeType } @@ -4626,7 +4626,7 @@ type ExposureEventToPhenotypicFeatureAssociation implements EntityToPhenotypicFe description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -4642,7 +4642,7 @@ type ExposureEventToPhenotypicFeatureAssociation implements EntityToPhenotypicFe agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -4661,39 +4661,39 @@ type ExposureEventToPhenotypicFeatureAssociation implements EntityToPhenotypicFe adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: ExposureEvent! frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease sexQualifier: BiologicalSex - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float } interface FeatureOrDiseaseQualifiersToEntityMixin { frequencyQualifier: FrequencyValue subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String } type Food @@ -4706,13 +4706,13 @@ type Food hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -4740,13 +4740,13 @@ type FoodAdditive hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -4765,16 +4765,16 @@ interface FrequencyQualifierMixin { frequencyQualifier: FrequencyValue subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } interface FrequencyQuantifier { - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float } type FunctionalAssociation @@ -4785,7 +4785,7 @@ type FunctionalAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -4800,7 +4800,7 @@ type FunctionalAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -4819,13 +4819,13 @@ type FunctionalAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: MacromolecularMachineMixin! object: OntologyClass! } @@ -4839,19 +4839,19 @@ type Fungus description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] } -type Gene implements GeneOrGeneProduct, GenomicEntity, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, OntologyClass +type Gene implements GeneOrGeneProduct, GeneOrGeneProductOrGeneFamily, GenomicEntity, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, OntologyClass { id: String! iri: IriType @@ -4863,14 +4863,14 @@ type Gene implements GeneOrGeneProduct, GenomicEntity, ChemicalEntityOrGeneOrGen providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType symbol: String - xref: [Uriorcurie] + xref: [String] hasBiologicalSequence: BiologicalSequence } @@ -4896,7 +4896,7 @@ type GeneAffectsChemicalAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -4915,13 +4915,13 @@ type GeneAffectsChemicalAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subjectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum subjectPartQualifier: GeneOrGeneProductOrChemicalPartQualifierEnum subjectDerivativeQualifier: String @@ -4936,10 +4936,10 @@ type GeneAffectsChemicalAssociation objectDerivativeQualifier: ChemicalEntityDerivativeEnum causalMechanismQualifier: CausalMechanismQualifierEnum anatomicalContextQualifier: [AnatomicalEntity] - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String speciesContextQualifier: OrganismTaxon subject: GeneOrGeneProduct! - predicate: Uriorcurie! + predicate: String! object: ChemicalEntity! } @@ -4965,7 +4965,7 @@ type GeneAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMixin, agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -4984,18 +4984,18 @@ type GeneAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMixin, adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subjectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum objectDirectionQualifier: DirectionQualifierEnum allelicRequirement: String - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseasesConfidenceScore: Float gene2phenotypeConfidenceCategory: String object: Disease! @@ -5015,7 +5015,7 @@ interface GeneExpressionMixin phenotypicState: DiseaseOrPhenotypicFeature } -type GeneFamily implements GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct +type GeneFamily implements GeneGroupingMixin, GeneOrGeneProductOrGeneFamily, ChemicalEntityOrGeneOrGeneProduct { id: String! iri: IriType @@ -5025,13 +5025,13 @@ type GeneFamily implements GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasGeneOrGeneProduct: [Gene] @@ -5059,7 +5059,7 @@ type GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5078,16 +5078,16 @@ type GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: Gene! object: GeneFamily! - predicate: Uriorcurie! + predicate: String! } interface GeneGroupingMixin @@ -5117,7 +5117,7 @@ type GeneHasVariantThatContributesToDiseaseAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5136,17 +5136,17 @@ type GeneHasVariantThatContributesToDiseaseAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum objectDirectionQualifier: DirectionQualifierEnum allelicRequirement: String - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseasesConfidenceScore: Float gene2phenotypeConfidenceCategory: String subjectFormOrVariantQualifier: String @@ -5162,6 +5162,7 @@ interface GeneOrGeneProduct interface GeneOrGeneProductOrGeneFamily { + name: SymbolType } type GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation @@ -5172,7 +5173,7 @@ type GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -5187,7 +5188,7 @@ type GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5206,13 +5207,13 @@ type GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: GeneOrGeneProductOrGeneFamily! object: AnatomicalEntity! } @@ -5239,7 +5240,7 @@ type GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5258,30 +5259,30 @@ type GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: GeneOrGeneProductOrGeneFamily! object: BiologicalProcessOrActivity! - predicate: Uriorcurie! + predicate: String! } interface GeneProductIsoformMixin { name: SymbolType synonym: [LabelType] - xref: [Uriorcurie] + xref: [String] } interface GeneProductMixin { name: SymbolType synonym: [LabelType] - xref: [Uriorcurie] + xref: [String] } type GeneRegulatesGeneAssociation @@ -5306,7 +5307,7 @@ type GeneRegulatesGeneAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5325,19 +5326,19 @@ type GeneRegulatesGeneAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] objectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum! objectDirectionQualifier: DirectionQualifierEnum! - qualifiedPredicate: Uriorcurie! + qualifiedPredicate: String! speciesContextQualifier: OrganismTaxon subject: GeneOrGeneProduct! - predicate: Uriorcurie! + predicate: String! object: GeneOrGeneProduct! } @@ -5363,7 +5364,7 @@ type GeneToDiseaseAssociation implements GeneToEntityAssociationMixin agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5382,18 +5383,18 @@ type GeneToDiseaseAssociation implements GeneToEntityAssociationMixin adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subjectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum objectDirectionQualifier: DirectionQualifierEnum allelicRequirement: String - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseasesConfidenceScore: Float gene2phenotypeConfidenceCategory: String subject: GeneOrGeneProduct! @@ -5404,7 +5405,7 @@ type GeneToDiseaseAssociation implements GeneToEntityAssociationMixin interface GeneToEntityAssociationMixin { subject: GeneOrGeneProduct! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -5430,7 +5431,7 @@ type GeneToExpressionSiteAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5449,19 +5450,19 @@ type GeneToExpressionSiteAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] stageQualifier: LifeStage quantifierQualifier: OntologyClass - objectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: String subject: GeneOrGeneProduct! object: AnatomicalEntity! - predicate: Uriorcurie! + predicate: String! } interface GeneToGeneAssociation @@ -5472,7 +5473,7 @@ interface GeneToGeneAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -5487,7 +5488,7 @@ interface GeneToGeneAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5506,13 +5507,13 @@ interface GeneToGeneAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: GeneOrGeneProduct! object: GeneOrGeneProduct! } @@ -5539,7 +5540,7 @@ type GeneToGeneCoexpressionAssociation implements GeneExpressionMixin agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5558,16 +5559,16 @@ type GeneToGeneCoexpressionAssociation implements GeneExpressionMixin adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: GeneOrGeneProduct! object: GeneOrGeneProduct! - predicate: Uriorcurie! + predicate: String! quantifierQualifier: OntologyClass expressionSite: AnatomicalEntity stageQualifier: LifeStage @@ -5596,7 +5597,7 @@ type GeneToGeneFamilyAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5615,16 +5616,16 @@ type GeneToGeneFamilyAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: Gene! object: GeneFamily! - predicate: Uriorcurie! + predicate: String! } type GeneToGeneHomologyAssociation @@ -5649,7 +5650,7 @@ type GeneToGeneHomologyAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5668,15 +5669,15 @@ type GeneToGeneHomologyAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: GeneOrGeneProduct! - predicate: Uriorcurie! + predicate: String! object: GeneOrGeneProduct! } @@ -5702,7 +5703,7 @@ type GeneToGeneProductRelationship agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5721,16 +5722,16 @@ type GeneToGeneProductRelationship adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: Gene! object: GeneProductMixin! - predicate: Uriorcurie! + predicate: String! } type GeneToGoTermAssociation @@ -5741,7 +5742,7 @@ type GeneToGoTermAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -5756,7 +5757,7 @@ type GeneToGoTermAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5775,13 +5776,13 @@ type GeneToGoTermAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: Gene! object: OntologyClass! } @@ -5794,7 +5795,7 @@ type GeneToPathwayAssociation implements GeneToEntityAssociationMixin description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -5809,7 +5810,7 @@ type GeneToPathwayAssociation implements GeneToEntityAssociationMixin agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5828,13 +5829,13 @@ type GeneToPathwayAssociation implements GeneToEntityAssociationMixin adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: GeneOrGeneProduct! object: Pathway! } @@ -5861,7 +5862,7 @@ type GeneToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -5880,13 +5881,13 @@ type GeneToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subjectFormOrVariantQualifier: ChemicalOrGeneOrGeneProductFormOrVariantEnum subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum objectDirectionQualifier: DirectionQualifierEnum @@ -5897,13 +5898,13 @@ type GeneToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso frequencyQualifier: FrequencyValue subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease sexQualifier: BiologicalSex - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float } type GeneticInheritance @@ -5916,13 +5917,13 @@ type GeneticInheritance hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -5937,13 +5938,13 @@ type Genome implements GenomicEntity, PhysicalEssence, OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasBiologicalSequence: BiologicalSequence @@ -5958,20 +5959,20 @@ type GenomicBackgroundExposure implements GeneGroupingMixin, PhysicalEssence, Ge hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -6008,7 +6009,7 @@ type GenomicSequenceLocalization agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -6027,21 +6028,21 @@ type GenomicSequenceLocalization adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - startInterbaseCoordinate: Integer - endInterbaseCoordinate: Integer + category: [String] + startInterbaseCoordinate: Int + endInterbaseCoordinate: Int genomeBuild: StrandEnum strand: StrandEnum phase: PhaseEnum subject: NucleicAcidEntity! object: NucleicAcidEntity! - predicate: Uriorcurie! + predicate: String! } type Genotype implements PhysicalEssence, GenomicEntity, OntologyClass @@ -6054,13 +6055,13 @@ type Genotype implements PhysicalEssence, GenomicEntity, OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasZygosity: Zygosity @@ -6089,7 +6090,7 @@ type GenotypeAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -6108,21 +6109,21 @@ type GenotypeAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! object: NamedThing! frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease subject: Genotype! } @@ -6149,7 +6150,7 @@ type GenotypeToDiseaseAssociation implements GenotypeToEntityAssociationMixin, E agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -6168,29 +6169,29 @@ type GenotypeToDiseaseAssociation implements GenotypeToEntityAssociationMixin, E adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease } interface GenotypeToEntityAssociationMixin { subject: Genotype! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -6216,7 +6217,7 @@ type GenotypeToGeneAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -6235,14 +6236,14 @@ type GenotypeToGeneAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! subject: Genotype! object: Gene! } @@ -6269,7 +6270,7 @@ type GenotypeToGenotypePartAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -6288,14 +6289,14 @@ type GenotypeToGenotypePartAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! subject: Genotype! object: Genotype! } @@ -6323,7 +6324,7 @@ type GenotypeToPhenotypicFeatureAssociation implements EntityToPhenotypicFeature agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -6342,27 +6343,27 @@ type GenotypeToPhenotypicFeatureAssociation implements EntityToPhenotypicFeature adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! subject: Genotype! frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease sexQualifier: BiologicalSex - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float } type GenotypeToVariantAssociation @@ -6387,7 +6388,7 @@ type GenotypeToVariantAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -6406,14 +6407,14 @@ type GenotypeToVariantAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! subject: Genotype! object: SequenceVariant! } @@ -6426,13 +6427,13 @@ type GenotypicSex hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -6449,20 +6450,20 @@ type GeographicExposure hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -6478,13 +6479,13 @@ type GeographicLocation hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! latitude: Float longitude: Float } @@ -6499,13 +6500,13 @@ type GeographicLocationAtTime hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! latitude: Float longitude: Float timepoint: TimeType @@ -6520,13 +6521,13 @@ type GrossAnatomicalStructure description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -6542,13 +6543,13 @@ type Haplotype implements GenomicEntity, PhysicalEssence, OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasBiologicalSequence: BiologicalSequence @@ -6564,13 +6565,13 @@ type Hospitalization hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type HospitalizationOutcome implements Outcome @@ -6586,13 +6587,13 @@ type Human implements SubjectOfInvestigation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -6608,17 +6609,17 @@ type IceesStudyResult hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! chiSquaredStatistic: Float - chiSquaredDof: Integer + chiSquaredDof: Int chiSquaredP: Float - totalSampleSize: Integer + totalSampleSize: Int fisherExactOddsRatio: Float fisherExactP: Float logOddsRatio: Float @@ -6634,13 +6635,13 @@ type IndividualOrganism implements SubjectOfInvestigation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -6656,17 +6657,17 @@ interface InformationContentEntity hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String } type InformationContentEntityToNamedThingAssociation @@ -6691,7 +6692,7 @@ type InformationContentEntityToNamedThingAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -6710,16 +6711,16 @@ type InformationContentEntityToNamedThingAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: NamedThing! object: NamedThing! - predicate: Uriorcurie! + predicate: String! } type Invertebrate @@ -6731,13 +6732,13 @@ type Invertebrate description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -6753,24 +6754,24 @@ type JournalArticle providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String authors: [Agent] pages: [String] summary: String keywords: [String] - meshTerms: [Uriorcurie] - xref: [Uriorcurie] + meshTerms: [String] + xref: [String] publicationType: [String]! id: String! name: LabelType - publishedIn: Uriorcurie! + publishedIn: String! isoAbbreviation: String volume: String issue: String @@ -6797,13 +6798,13 @@ type LifeStage implements OntologyClass description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -6819,13 +6820,13 @@ type LogOddsAnalysisResult hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type MacromolecularComplex implements MacromolecularMachineMixin @@ -6838,13 +6839,13 @@ type MacromolecularComplex implements MacromolecularMachineMixin hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -6871,7 +6872,7 @@ type MacromolecularMachineHasSubstrateAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -6890,15 +6891,15 @@ type MacromolecularMachineHasSubstrateAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: MacromolecularMachineMixin! - predicate: Uriorcurie! + predicate: String! object: ChemicalEntityOrProteinOrPolypeptide! } @@ -6915,7 +6916,7 @@ type MacromolecularMachineToBiologicalProcessAssociation implements Macromolecul description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -6930,7 +6931,7 @@ type MacromolecularMachineToBiologicalProcessAssociation implements Macromolecul agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -6949,13 +6950,13 @@ type MacromolecularMachineToBiologicalProcessAssociation implements Macromolecul adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: MacromolecularMachineMixin! object: BiologicalProcess! speciesContextQualifier: OrganismTaxon @@ -6969,7 +6970,7 @@ type MacromolecularMachineToCellularComponentAssociation implements Macromolecul description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -6984,7 +6985,7 @@ type MacromolecularMachineToCellularComponentAssociation implements Macromolecul agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7003,13 +7004,13 @@ type MacromolecularMachineToCellularComponentAssociation implements Macromolecul adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: MacromolecularMachineMixin! object: CellularComponent! speciesContextQualifier: OrganismTaxon @@ -7018,7 +7019,7 @@ type MacromolecularMachineToCellularComponentAssociation implements Macromolecul interface MacromolecularMachineToEntityAssociationMixin { subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! speciesContextQualifier: OrganismTaxon } @@ -7031,7 +7032,7 @@ type MacromolecularMachineToMolecularActivityAssociation implements Macromolecul description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -7046,7 +7047,7 @@ type MacromolecularMachineToMolecularActivityAssociation implements Macromolecul agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7065,13 +7066,13 @@ type MacromolecularMachineToMolecularActivityAssociation implements Macromolecul adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: MacromolecularMachineMixin! object: MolecularActivity! speciesContextQualifier: OrganismTaxon @@ -7086,13 +7087,13 @@ type Mammal implements SubjectOfInvestigation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -7113,13 +7114,13 @@ type MaterialSample implements SubjectOfInvestigation hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type MaterialSampleDerivationAssociation @@ -7144,7 +7145,7 @@ type MaterialSampleDerivationAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7163,15 +7164,15 @@ type MaterialSampleDerivationAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: MaterialSample! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -7184,7 +7185,7 @@ type MaterialSampleToDiseaseOrPhenotypicFeatureAssociation implements MaterialSa hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -7200,7 +7201,7 @@ type MaterialSampleToDiseaseOrPhenotypicFeatureAssociation implements MaterialSa agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7219,23 +7220,23 @@ type MaterialSampleToDiseaseOrPhenotypicFeatureAssociation implements MaterialSa adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] diseaseContextQualifier: Disease - subjectSpecializationQualifier: Uriorcurie - objectSpecializationQualifier: Uriorcurie + subjectSpecializationQualifier: String + objectSpecializationQualifier: String anatomicalContextQualifier: [String] } interface MaterialSampleToEntityAssociationMixin { subject: MaterialSample! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -7249,13 +7250,13 @@ type MicroRNA hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -7263,7 +7264,7 @@ type MicroRNA interface ModelToDiseaseAssociationMixin { subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -7277,13 +7278,13 @@ type MolecularActivity implements Occurrent, OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasInput: [MolecularEntity] @@ -7299,7 +7300,7 @@ type MolecularActivityToChemicalEntityAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -7314,7 +7315,7 @@ type MolecularActivityToChemicalEntityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7333,13 +7334,13 @@ type MolecularActivityToChemicalEntityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: MolecularActivity! object: ChemicalEntity! } @@ -7352,7 +7353,7 @@ type MolecularActivityToMolecularActivityAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -7367,7 +7368,7 @@ type MolecularActivityToMolecularActivityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7386,13 +7387,13 @@ type MolecularActivityToMolecularActivityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: MolecularActivity! object: MolecularActivity! } @@ -7419,7 +7420,7 @@ type MolecularActivityToPathwayAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7438,16 +7439,16 @@ type MolecularActivityToPathwayAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: MolecularActivity! object: Pathway! - predicate: Uriorcurie! + predicate: String! } type MolecularEntity implements OntologyClass @@ -7460,13 +7461,13 @@ type MolecularEntity implements OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -7492,13 +7493,13 @@ type MolecularMixture hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -7530,13 +7531,13 @@ type NamedThing hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type NamedThingAssociatedWithLikelihoodOfNamedThingAssociation @@ -7561,7 +7562,7 @@ type NamedThingAssociatedWithLikelihoodOfNamedThingAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7580,17 +7581,17 @@ type NamedThingAssociatedWithLikelihoodOfNamedThingAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: NamedThing! subjectAspectQualifier: String subjectContextQualifier: OntologyClass - predicate: Uriorcurie! + predicate: String! object: NamedThing! objectAspectQualifier: String objectContextQualifier: OntologyClass @@ -7611,13 +7612,13 @@ type NoncodingRNAProduct hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -7632,13 +7633,13 @@ type NucleicAcidEntity implements GenomicEntity, ThingWithTaxon, PhysicalEssence hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -7667,13 +7668,13 @@ type NucleicAcidSequenceMotif hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -7688,13 +7689,13 @@ type NucleosomeModification implements GeneProductIsoformMixin, GenomicEntity, E hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasBiologicalSequence: BiologicalSequence @@ -7710,13 +7711,13 @@ type ObservedExpectedFrequencyAnalysisResult hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } interface Occurrent @@ -7731,13 +7732,13 @@ type Onset hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -7758,13 +7759,13 @@ type OrganismAttribute hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -7782,20 +7783,20 @@ type OrganismTaxon hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! hasTaxonomicRank: TaxonomicRank } interface OrganismTaxonToEntityAssociation { subject: OrganismTaxon! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -7821,7 +7822,7 @@ type OrganismTaxonToEnvironmentAssociation implements OrganismTaxonToEntityAssoc agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7840,16 +7841,16 @@ type OrganismTaxonToEnvironmentAssociation implements OrganismTaxonToEntityAssoc adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: OrganismTaxon! object: NamedThing! - predicate: Uriorcurie! + predicate: String! } type OrganismTaxonToOrganismTaxonAssociation implements OrganismTaxonToEntityAssociation @@ -7860,7 +7861,7 @@ type OrganismTaxonToOrganismTaxonAssociation implements OrganismTaxonToEntityAss description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -7875,7 +7876,7 @@ type OrganismTaxonToOrganismTaxonAssociation implements OrganismTaxonToEntityAss agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7894,13 +7895,13 @@ type OrganismTaxonToOrganismTaxonAssociation implements OrganismTaxonToEntityAss adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: OrganismTaxon! object: OrganismTaxon! } @@ -7927,7 +7928,7 @@ type OrganismTaxonToOrganismTaxonInteraction agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -7946,17 +7947,17 @@ type OrganismTaxonToOrganismTaxonInteraction adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] associatedEnvironmentalContext: String subject: OrganismTaxon! object: OrganismTaxon! - predicate: Uriorcurie! + predicate: String! } type OrganismTaxonToOrganismTaxonSpecialization @@ -7981,7 +7982,7 @@ type OrganismTaxonToOrganismTaxonSpecialization agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -8000,16 +8001,16 @@ type OrganismTaxonToOrganismTaxonSpecialization adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: OrganismTaxon! object: OrganismTaxon! - predicate: Uriorcurie! + predicate: String! } type OrganismToOrganismAssociation @@ -8020,7 +8021,7 @@ type OrganismToOrganismAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -8035,7 +8036,7 @@ type OrganismToOrganismAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -8054,13 +8055,13 @@ type OrganismToOrganismAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: IndividualOrganism! object: IndividualOrganism! } @@ -8074,13 +8075,13 @@ type OrganismalEntity implements SubjectOfInvestigation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -8094,7 +8095,7 @@ type OrganismalEntityAsAModelOfDiseaseAssociation implements ModelToDiseaseAssoc description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -8110,7 +8111,7 @@ type OrganismalEntityAsAModelOfDiseaseAssociation implements ModelToDiseaseAssoc agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -8129,20 +8130,20 @@ type OrganismalEntityAsAModelOfDiseaseAssociation implements ModelToDiseaseAssoc adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: OrganismalEntity! frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease } @@ -8172,7 +8173,7 @@ type PairwiseGeneToGeneInteraction agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -8191,16 +8192,16 @@ type PairwiseGeneToGeneInteraction adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: GeneOrGeneProduct! object: GeneOrGeneProduct! - predicate: Uriorcurie! + predicate: String! } type PairwiseMolecularInteraction @@ -8224,7 +8225,7 @@ type PairwiseMolecularInteraction agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -8243,17 +8244,17 @@ type PairwiseMolecularInteraction adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] interactingMoleculesCategory: OntologyClass subject: MolecularEntity! id: String! - predicate: Uriorcurie! + predicate: String! object: MolecularEntity! } @@ -8267,20 +8268,20 @@ type Patent providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String authors: [Agent] pages: [String] summary: String keywords: [String] - meshTerms: [Uriorcurie] - xref: [Uriorcurie] + meshTerms: [String] + xref: [String] publicationType: [String]! id: String! name: LabelType @@ -8299,20 +8300,20 @@ type PathologicalAnatomicalExposure hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -8331,13 +8332,13 @@ type PathologicalAnatomicalStructure implements PathologicalEntityMixin description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -8357,13 +8358,13 @@ type PathologicalProcess implements PathologicalEntityMixin hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasInput: [NamedThing] @@ -8380,20 +8381,20 @@ type PathologicalProcessExposure hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -8413,13 +8414,13 @@ type Pathway implements OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasInput: [NamedThing] @@ -8437,13 +8438,13 @@ type Phenomenon implements Occurrent hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type PhenotypicFeature @@ -8456,13 +8457,13 @@ type PhenotypicFeature hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType inheritance: GeneticInheritance @@ -8492,7 +8493,7 @@ type PhenotypicFeatureToDiseaseAssociation implements EntityToDiseaseAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -8511,44 +8512,44 @@ type PhenotypicFeatureToDiseaseAssociation implements EntityToDiseaseAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease sexQualifier: BiologicalSex - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float } type PhenotypicFeatureToEntityAssociationMixin implements FrequencyQuantifier { frequencyQualifier: FrequencyValue - predicate: Uriorcurie! + predicate: String! object: NamedThing! subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String sexQualifier: BiologicalSex subject: PhenotypicFeature! - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float } type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatureToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin @@ -8560,7 +8561,7 @@ type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatur hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -8576,7 +8577,7 @@ type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatur agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -8595,24 +8596,24 @@ type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatur adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String sexQualifier: BiologicalSex - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float diseaseContextQualifier: Disease } @@ -8624,13 +8625,13 @@ type PhenotypicQuality hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -8646,13 +8647,13 @@ type PhenotypicSex hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -8670,13 +8671,13 @@ type PhysicalEntity implements PhysicalEssence hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } interface PhysicalEssence @@ -8697,13 +8698,13 @@ type PhysiologicalProcess implements OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasInput: [NamedThing] @@ -8721,13 +8722,13 @@ type PlanetaryEntity hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type Plant @@ -8739,13 +8740,13 @@ type Plant description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -8761,13 +8762,13 @@ type Polypeptide implements ChemicalEntityOrGeneOrGeneProduct, ChemicalEntityOrP hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -8781,13 +8782,13 @@ type PopulationOfIndividualOrganisms implements SubjectOfInvestigation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -8815,7 +8816,7 @@ type PopulationToPopulationAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -8834,16 +8835,16 @@ type PopulationToPopulationAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: PopulationOfIndividualOrganisms! object: PopulationOfIndividualOrganisms! - predicate: Uriorcurie! + predicate: String! } type PosttranslationalModification implements GeneProductIsoformMixin @@ -8856,13 +8857,13 @@ type PosttranslationalModification implements GeneProductIsoformMixin hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -8876,8 +8877,8 @@ type PredicateMapping subjectPartQualifier: String subjectDerivativeQualifier: String subjectContextQualifier: String - predicate: Uriorcurie! - qualifiedPredicate: Uriorcurie + predicate: String! + qualifiedPredicate: String objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum objectFormOrVariantQualifier: String @@ -8902,20 +8903,20 @@ type PreprintPublication providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String authors: [Agent] pages: [String] summary: String keywords: [String] - meshTerms: [Uriorcurie] - xref: [Uriorcurie] + meshTerms: [String] + xref: [String] publicationType: [String]! id: String! name: LabelType @@ -8931,13 +8932,13 @@ type Procedure implements ActivityAndBehavior hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type ProcessRegulatesProcessAssociation @@ -8962,7 +8963,7 @@ type ProcessRegulatesProcessAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -8981,15 +8982,15 @@ type ProcessRegulatesProcessAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: BiologicalProcess! - predicate: Uriorcurie! + predicate: String! object: BiologicalProcess! } @@ -9003,13 +9004,13 @@ type ProcessedMaterial hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -9037,13 +9038,13 @@ type Protein implements GeneProductMixin hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -9058,13 +9059,13 @@ type ProteinDomain implements GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProdu hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasGeneOrGeneProduct: [Gene] @@ -9080,13 +9081,13 @@ type ProteinFamily implements GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProdu hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasGeneOrGeneProduct: [Gene] @@ -9102,13 +9103,13 @@ type ProteinIsoform implements GeneProductIsoformMixin hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -9123,20 +9124,20 @@ type Publication providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String authors: [Agent] pages: [String] summary: String keywords: [String] - meshTerms: [Uriorcurie] - xref: [Uriorcurie] + meshTerms: [String] + xref: [String] publicationType: [String]! id: String! name: LabelType @@ -9145,7 +9146,7 @@ type Publication type QuantityValue { hasUnit: Unit - hasNumericValue: Double + hasNumericValue: Float } type ReactionToCatalystAssociation @@ -9170,7 +9171,7 @@ type ReactionToCatalystAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -9189,16 +9190,16 @@ type ReactionToCatalystAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! speciesContextQualifier: OrganismTaxon - stoichiometry: Integer + stoichiometry: Int reactionDirection: ReactionDirectionEnum reactionSide: ReactionSideEnum subject: MolecularEntity! @@ -9227,7 +9228,7 @@ type ReactionToParticipantAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -9246,17 +9247,17 @@ type ReactionToParticipantAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! object: ChemicalEntity! speciesContextQualifier: OrganismTaxon - stoichiometry: Integer + stoichiometry: Int reactionDirection: ReactionDirectionEnum reactionSide: ReactionSideEnum subject: MolecularEntity! @@ -9272,13 +9273,13 @@ type ReagentTargetedGene implements GenomicEntity, PhysicalEssence, OntologyClas hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasBiologicalSequence: BiologicalSequence @@ -9294,13 +9295,13 @@ type RegulatoryRegion implements GenomicEntity, ChemicalEntityOrGeneOrGeneProduc hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasBiologicalSequence: BiologicalSequence @@ -9325,13 +9326,13 @@ type RelativeFrequencyAnalysisResult hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type RetrievalSource @@ -9346,19 +9347,19 @@ type RetrievalSource providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date - resourceId: Uriorcurie! + creationDate: String + resourceId: String! resourceRole: ResourceRoleEnum! - upstreamResourceIds: [Uriorcurie] - sourceRecordUrls: [Uriorcurie] - xref: [Uriorcurie] + upstreamResourceIds: [String] + sourceRecordUrls: [String] + xref: [String] } type RNAProduct implements GeneProductMixin @@ -9371,13 +9372,13 @@ type RNAProduct implements GeneProductMixin hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -9392,13 +9393,13 @@ type RNAProductIsoform implements GeneProductIsoformMixin hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -9416,7 +9417,7 @@ type SequenceAssociation hasAttribute: [Attribute] deprecated: Boolean subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -9432,7 +9433,7 @@ type SequenceAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -9451,13 +9452,13 @@ type SequenceAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] } type SequenceFeatureRelationship @@ -9468,7 +9469,7 @@ type SequenceFeatureRelationship description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -9483,7 +9484,7 @@ type SequenceFeatureRelationship agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -9502,13 +9503,13 @@ type SequenceFeatureRelationship adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: NucleicAcidEntity! object: NucleicAcidEntity! } @@ -9522,13 +9523,13 @@ type SequenceVariant implements GenomicEntity, PhysicalEssence, OntologyClass hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasGene: [Gene] @@ -9545,7 +9546,7 @@ interface SequenceVariantModulatesTreatmentAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -9560,7 +9561,7 @@ interface SequenceVariantModulatesTreatmentAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -9579,13 +9580,13 @@ interface SequenceVariantModulatesTreatmentAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: SequenceVariant! object: Treatment! } @@ -9599,20 +9600,20 @@ type Serial providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String authors: [Agent] pages: [String] summary: String keywords: [String] - meshTerms: [Uriorcurie] - xref: [Uriorcurie] + meshTerms: [String] + xref: [String] publicationType: [String]! name: LabelType isoAbbreviation: String @@ -9630,13 +9631,13 @@ type SeverityValue hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -9654,13 +9655,13 @@ type SiRNA hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -9675,13 +9676,13 @@ type SmallMolecule hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! tradeName: String availableFrom: [DrugAvailabilityEnum] maxToleratedDose: String @@ -9706,13 +9707,13 @@ type Snv hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasGene: [Gene] @@ -9729,13 +9730,13 @@ type SocioeconomicAttribute hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] @@ -9751,20 +9752,20 @@ type SocioeconomicExposure description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -9789,13 +9790,13 @@ type Study hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! hasStudyResults: [StudyResult] } @@ -9808,13 +9809,13 @@ type StudyPopulation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -9830,13 +9831,13 @@ interface StudyResult hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! } type StudyVariable @@ -9849,17 +9850,17 @@ type StudyVariable hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String } interface SubjectOfInvestigation @@ -9874,7 +9875,7 @@ type TaxonToTaxonAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -9889,7 +9890,7 @@ type TaxonToTaxonAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -9908,13 +9909,13 @@ type TaxonToTaxonAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: OrganismTaxon! object: OrganismTaxon! } @@ -9934,19 +9935,19 @@ type TextMiningStudyResult hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! supportingText: [String] - subjectLocationInText: [Integer] - objectLocationInText: [Integer] + subjectLocationInText: [Int] + objectLocationInText: [Int] extractionConfidenceScore: Float supportingDocumentType: String - supportingDocumentYear: Integer + supportingDocumentYear: Int supportingTextSectionType: String } @@ -9966,13 +9967,13 @@ type Transcript hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType } @@ -9985,7 +9986,7 @@ type TranscriptToGeneRelationship description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -10000,7 +10001,7 @@ type TranscriptToGeneRelationship agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -10019,13 +10020,13 @@ type TranscriptToGeneRelationship adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: Transcript! object: Gene! } @@ -10040,13 +10041,13 @@ type TranscriptionFactorBindingSite implements GenomicEntity, ChemicalEntityOrGe hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasBiologicalSequence: BiologicalSequence @@ -10061,20 +10062,20 @@ type Treatment implements ChemicalOrDrugOrTreatment hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! timepoint: TimeType exposureType: String exposureVehicle: String exposureRoute: String - exposureStartAge: Integer - exposureEndAge: Integer - exposureDuration: Time + exposureStartAge: Int + exposureEndAge: Int + exposureDuration: String exposureMagnitude: String exposureAdditionalCondition: String id: String! @@ -10105,7 +10106,7 @@ type VariantAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMix agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -10124,21 +10125,21 @@ type VariantAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMix adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] - predicate: Uriorcurie! + category: [String] + predicate: String! object: NamedThing! frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease subject: SequenceVariant! } @@ -10165,7 +10166,7 @@ type VariantToDiseaseAssociation implements VariantToEntityAssociationMixin, Ent agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -10184,29 +10185,29 @@ type VariantToDiseaseAssociation implements VariantToEntityAssociationMixin, Ent adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: NamedThing! - predicate: Uriorcurie! + predicate: String! object: NamedThing! frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease } interface VariantToEntityAssociationMixin { subject: SequenceVariant! - predicate: Uriorcurie! + predicate: String! object: NamedThing! } @@ -10233,7 +10234,7 @@ type VariantToGeneAssociation implements VariantToEntityAssociationMixin agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -10252,15 +10253,15 @@ type VariantToGeneAssociation implements VariantToEntityAssociationMixin adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] object: Gene! - predicate: Uriorcurie! + predicate: String! } type VariantToGeneExpressionAssociation implements GeneExpressionMixin @@ -10286,7 +10287,7 @@ type VariantToGeneExpressionAssociation implements GeneExpressionMixin agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -10305,15 +10306,15 @@ type VariantToGeneExpressionAssociation implements GeneExpressionMixin adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] object: Gene! - predicate: Uriorcurie! + predicate: String! quantifierQualifier: OntologyClass expressionSite: AnatomicalEntity stageQualifier: LifeStage @@ -10328,7 +10329,7 @@ type VariantToPhenotypicFeatureAssociation implements VariantToEntityAssociation description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! object: NamedThing! negated: Boolean qualifier: String @@ -10344,7 +10345,7 @@ type VariantToPhenotypicFeatureAssociation implements VariantToEntityAssociation agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -10363,26 +10364,26 @@ type VariantToPhenotypicFeatureAssociation implements VariantToEntityAssociation adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: SequenceVariant! frequencyQualifier: FrequencyValue subjectAspectQualifier: String subjectDirectionQualifier: DirectionQualifierEnum objectAspectQualifier: String objectDirectionQualifier: DirectionQualifierEnum - qualifiedPredicate: Uriorcurie + qualifiedPredicate: String diseaseContextQualifier: Disease sexQualifier: BiologicalSex - hasCount: Integer - hasTotal: Integer - hasQuotient: Double - hasPercentage: Double + hasCount: Int + hasTotal: Int + hasQuotient: Float + hasPercentage: Float } type VariantToPopulationAssociation implements VariantToEntityAssociationMixin, FrequencyQuantifier, FrequencyQualifierMixin @@ -10393,7 +10394,7 @@ type VariantToPopulationAssociation implements VariantToEntityAssociationMixin, description: NarrativeText hasAttribute: [Attribute] deprecated: Boolean - predicate: Uriorcurie! + predicate: String! negated: Boolean qualifier: String qualifiers: [OntologyClass] @@ -10408,7 +10409,7 @@ type VariantToPopulationAssociation implements VariantToEntityAssociationMixin, agentType: AgentTypeEnum! timepoint: TimeType originalSubject: String - originalPredicate: Uriorcurie + originalPredicate: String originalObject: String subjectFeatureName: String objectFeatureName: String @@ -10427,19 +10428,19 @@ type VariantToPopulationAssociation implements VariantToEntityAssociationMixin, adjustedPValue: Float supportingText: [String] hasSupportingStudies: [Study] - updateDate: Date + updateDate: String hasConfidenceScore: Float elevateToPrediction: Boolean - evidenceCount: Integer - semmedAgreementCount: Integer + evidenceCount: Int + semmedAgreementCount: Int type: [String] - category: [Uriorcurie] + category: [String] subject: SequenceVariant! object: PopulationOfIndividualOrganisms! - hasQuotient: Double - hasCount: Integer - hasTotal: Integer - hasPercentage: Double + hasQuotient: Float + hasCount: Int + hasTotal: Int + hasPercentage: Float frequencyQualifier: FrequencyValue } @@ -10452,13 +10453,13 @@ type Vertebrate description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -10473,13 +10474,13 @@ type Virus implements SubjectOfInvestigation description: NarrativeText deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! inTaxon: [OrganismTaxon] inTaxonLabel: LabelType hasAttribute: [Attribute] @@ -10495,20 +10496,20 @@ type WebPage providedBy: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! license: String rights: String format: String - creationDate: Date + creationDate: String authors: [Agent] pages: [String] summary: String keywords: [String] - meshTerms: [Uriorcurie] - xref: [Uriorcurie] + meshTerms: [String] + xref: [String] publicationType: [String]! id: String! name: LabelType @@ -10522,13 +10523,13 @@ type Zygosity hasAttribute: [Attribute] deprecated: Boolean providedBy: [String] - xref: [Uriorcurie] + xref: [String] fullName: LabelType synonym: [LabelType] - equivalentIdentifiers: [Uriorcurie] + equivalentIdentifiers: [String] informationContent: Float - taxon: Uriorcurie - category: [Uriorcurie]! + taxon: String + category: [String]! name: LabelType hasAttributeType: OntologyClass! hasQuantitativeValue: [QuantityValue] diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld index 66d4239e1..211d9e57d 100644 --- a/project/jsonld/biolink_model.context.jsonld +++ b/project/jsonld/biolink_model.context.jsonld @@ -1,9 +1,4 @@ { - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2026-04-21T19:05:22", - "source": "biolink_model.yaml" - }, "@context": { "xsd": "http://www.w3.org/2001/XMLSchema#", "AGRKB": "https://www.alliancegenome.org/", @@ -279,6 +274,10 @@ "@prefix": true }, "MIR": "http://identifiers.org/mir/", + "MOD": { + "@id": "http://purl.obolibrary.org/obo/MOD_", + "@prefix": true + }, "MONDO": { "@id": "http://purl.obolibrary.org/obo/MONDO_", "@prefix": true @@ -461,6 +460,7 @@ "@prefix": true }, "UNII": "http://identifiers.org/unii/", + "UNIMOD": "http://identifiers.org/unimod/", "UNIPROT.ISOFORM": "http://purl.uniprot.org/isoforms/", "UO-PROPERTY": "http://purl.obolibrary.org/obo/uo#", "UPHENO": { @@ -629,7 +629,7 @@ "@id": "adjusted_p_value" }, "adverse_event_of": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "adverse_event_of" }, "affected_by": { @@ -645,7 +645,7 @@ "@id": "affects_likelihood_of" }, "affects_sensitivity_to": { - "@type": "biolink:ChemicalEntityOrGeneOrGeneProduct", + "@type": "@id", "@id": "affects_sensitivity_to" }, "affiliation": { @@ -706,6 +706,11 @@ "@id": "applied_to_treat" }, "aspect_qualifier": { + "@context": { + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + }, "@id": "aspect_qualifier" }, "associated_environmental_context": { @@ -796,11 +801,11 @@ "@id": "can_be_carried_out_by" }, "capable_of": { - "@type": "biolink:Occurrent", + "@type": "@id", "@id": "capable_of" }, "catalyst_qualifier": { - "@type": "biolink:MacromolecularMachineMixin", + "@type": "@id", "@id": "catalyst_qualifier" }, "catalyzes": { @@ -985,7 +990,7 @@ "@id": "coexists_with" }, "coexpressed_with": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "coexpressed_with" }, "colocalizes_with": { @@ -1013,7 +1018,7 @@ "@id": "concept_pair_count" }, "condition_ameliorated_by": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "condition_ameliorated_by" }, "condition_associated_with_gene": { @@ -1021,19 +1026,19 @@ "@id": "condition_associated_with_gene" }, "condition_exacerbated_by": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "condition_exacerbated_by" }, "condition_predisposed_by": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "condition_predisposed_by" }, "condition_prevented_by": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "condition_prevented_by" }, "condition_promoted_by": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "condition_promoted_by" }, "consumed_by": { @@ -1098,7 +1103,7 @@ "@id": "decreases_amount_or_activity_of" }, "decreases_sensitivity_to": { - "@type": "biolink:ChemicalEntityOrGeneOrGeneProduct", + "@type": "@id", "@id": "decreases_sensitivity_to" }, "deprecated": { @@ -1204,7 +1209,7 @@ "@id": "druggable_gene_category" }, "edges": { - "@type": "biolink:Association", + "@type": "@id", "@id": "edges" }, "editor": { @@ -1288,7 +1293,7 @@ "@id": "expressed_in" }, "expresses": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "expresses" }, "expression_site": { @@ -1375,7 +1380,7 @@ "@id": "genome_build" }, "has_active_component": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "has_active_component" }, "has_active_ingredient": { @@ -1387,7 +1392,7 @@ "@id": "has_adverse_event" }, "has_affinity": { - "@type": "biolink:AffinityMeasurement", + "@type": "@id", "@id": "has_affinity" }, "has_attribute": { @@ -1418,11 +1423,11 @@ "@id": "has_biological_sex" }, "has_biomarker": { - "@type": "biolink:ChemicalEntityOrGeneOrGeneProduct", + "@type": "@id", "@id": "has_biomarker" }, "has_catalyst": { - "@type": "biolink:Occurrent", + "@type": "@id", "@id": "has_catalyst" }, "has_chemical_formula": { @@ -1448,7 +1453,7 @@ "@id": "has_constituent" }, "has_contraindication": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "has_contraindication" }, "has_contributor": { @@ -1512,7 +1517,7 @@ "@id": "has_gene_or_gene_product" }, "has_gene_product": { - "@type": "biolink:GeneProductMixin", + "@type": "@id", "@id": "has_gene_product" }, "has_increased_amount": { @@ -1552,11 +1557,11 @@ "@id": "has_nearby_variant" }, "has_negative_upstream_actor": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "has_negative_upstream_actor" }, "has_negative_upstream_or_within_actor": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "has_negative_upstream_or_within_actor" }, "has_non_coding_variant": { @@ -1588,7 +1593,7 @@ "@id": "has_part" }, "has_participant": { - "@type": "biolink:Occurrent", + "@type": "@id", "@id": "has_participant" }, "has_percentage": { @@ -1604,11 +1609,11 @@ "@id": "has_plasma_membrane_part" }, "has_positive_upstream_actor": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "has_positive_upstream_actor" }, "has_positive_upstream_or_within_actor": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "has_positive_upstream_or_within_actor" }, "has_procedure": { @@ -1628,7 +1633,7 @@ "@id": "has_qualitative_value" }, "has_quantitative_value": { - "@type": "biolink:QuantityValue", + "@type": "@id", "@id": "has_quantitative_value" }, "has_quotient": { @@ -1662,11 +1667,11 @@ "@id": "has_stressor" }, "has_study_results": { - "@type": "biolink:StudyResult", + "@type": "@id", "@id": "has_study_results" }, "has_substrate": { - "@type": "biolink:ChemicalEntityOrGeneOrGeneProduct", + "@type": "@id", "@id": "has_substrate" }, "has_supporting_studies": { @@ -1698,11 +1703,11 @@ "@id": "has_unit" }, "has_upstream_actor": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "has_upstream_actor" }, "has_upstream_or_within_actor": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "has_upstream_or_within_actor" }, "has_variant_part": { @@ -1729,7 +1734,7 @@ "@id": "homologous_to" }, "in_cell_population_with": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "in_cell_population_with" }, "in_clinical_trials_for": { @@ -1737,7 +1742,7 @@ "@id": "in_clinical_trials_for" }, "in_complex_with": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "in_complex_with" }, "in_linkage_disequilibrium_with": { @@ -1745,7 +1750,7 @@ "@id": "in_linkage_disequilibrium_with" }, "in_pathway_with": { - "@type": "biolink:GeneOrGeneProduct", + "@type": "@id", "@id": "in_pathway_with" }, "in_preclinical_trials_for": { @@ -1772,7 +1777,7 @@ "@id": "increases_amount_or_activity_of" }, "increases_sensitivity_to": { - "@type": "biolink:ChemicalEntityOrGeneOrGeneProduct", + "@type": "@id", "@id": "increases_sensitivity_to" }, "indirectly_physically_interacts_with": { @@ -1825,7 +1830,7 @@ "@id": "is_excipient_of" }, "is_frameshift_variant_of": { - "@type": "biolink:GenomicEntity", + "@type": "@id", "@id": "is_frameshift_variant_of" }, "is_input_of": { @@ -1841,7 +1846,7 @@ "@id": "is_metabolite_of" }, "is_missense_variant_of": { - "@type": "biolink:GenomicEntity", + "@type": "@id", "@id": "is_missense_variant_of" }, "is_molecular_consequence_of": { @@ -1849,15 +1854,15 @@ "@id": "is_molecular_consequence_of" }, "is_nearby_variant_of": { - "@type": "biolink:GenomicEntity", + "@type": "@id", "@id": "is_nearby_variant_of" }, "is_non_coding_variant_of": { - "@type": "biolink:GenomicEntity", + "@type": "@id", "@id": "is_non_coding_variant_of" }, "is_nonsense_variant_of": { - "@type": "biolink:GenomicEntity", + "@type": "@id", "@id": "is_nonsense_variant_of" }, "is_output_of": { @@ -1865,26 +1870,26 @@ "@id": "is_output_of" }, "is_sequence_variant_of": { - "@type": "biolink:GenomicEntity", + "@type": "@id", "@id": "is_sequence_variant_of" }, "is_side_effect_of": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "is_side_effect_of" }, "is_splice_site_variant_of": { - "@type": "biolink:GenomicEntity", + "@type": "@id", "@id": "is_splice_site_variant_of" }, "is_substrate_of": { - "@type": "biolink:ChemicalEntityOrGeneOrGeneProduct", + "@type": "@id", "@id": "is_substrate_of" }, "is_supplement": { "@id": "is_supplement" }, "is_synonymous_variant_of": { - "@type": "biolink:GenomicEntity", + "@type": "@id", "@id": "is_synonymous_variant_of" }, "is_toxic": { @@ -2025,7 +2030,7 @@ "@id": "models" }, "models_demonstrating_benefits_for": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "models_demonstrating_benefits_for" }, "name": { @@ -2053,7 +2058,7 @@ "@id": "node_property" }, "nodes": { - "@type": "biolink:Entity", + "@type": "@id", "@id": "nodes" }, "not_completed_by": { @@ -2073,6 +2078,11 @@ "@id": "rdf:object" }, "object_aspect_qualifier": { + "@context": { + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + }, "@id": "object_aspect_qualifier" }, "object_category": { @@ -2220,11 +2230,11 @@ "@id": "positively_correlated_with" }, "preceded_by": { - "@type": "biolink:Occurrent", + "@type": "@id", "@id": "preceded_by" }, "precedes": { - "@type": "biolink:Occurrent", + "@type": "@id", "@id": "precedes" }, "predicate": { @@ -2232,7 +2242,7 @@ "@id": "rdf:predicate" }, "predicate_mappings": { - "@type": "biolink:PredicateMapping", + "@type": "@id", "@id": "predicate_mappings" }, "predisposes_to_condition": { @@ -2320,11 +2330,11 @@ "@id": "reaction_side" }, "regulated_by": { - "@type": "biolink:PhysicalEssenceOrOccurrent", + "@type": "@id", "@id": "regulated_by" }, "regulates": { - "@type": "biolink:PhysicalEssenceOrOccurrent", + "@type": "@id", "@id": "regulates" }, "related_condition": { @@ -2426,7 +2436,7 @@ "@id": "semmed_agreement_count" }, "sensitivity_affected_by": { - "@type": "biolink:ChemicalEntityOrGeneOrGeneProduct", + "@type": "@id", "@id": "sensitivity_affected_by" }, "sensitivity_associated_with": { @@ -2434,11 +2444,11 @@ "@id": "sensitivity_associated_with" }, "sensitivity_decreased_by": { - "@type": "biolink:ChemicalEntityOrGeneOrGeneProduct", + "@type": "@id", "@id": "sensitivity_decreased_by" }, "sensitivity_increased_by": { - "@type": "biolink:ChemicalEntityOrGeneOrGeneProduct", + "@type": "@id", "@id": "sensitivity_increased_by" }, "sequence_localization_attribute": { @@ -2529,6 +2539,11 @@ "@id": "rdf:subject" }, "subject_aspect_qualifier": { + "@context": { + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + }, "@id": "subject_aspect_qualifier" }, "subject_category": { @@ -2573,7 +2588,7 @@ "@id": "subject_namespace" }, "subject_of_treatment_application_or_study_for_treatment_by": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "subject_of_treatment_application_or_study_for_treatment_by" }, "subject_part_qualifier": { @@ -2658,7 +2673,7 @@ "@id": "taxon" }, "taxon_of": { - "@type": "biolink:ThingWithTaxon", + "@type": "@id", "@id": "taxon_of" }, "temporal_context_qualifier": { @@ -2668,15 +2683,15 @@ "@id": "temporal_interval_qualifier" }, "temporally_related_to": { - "@type": "biolink:Occurrent", + "@type": "@id", "@id": "temporally_related_to" }, "tested_by_clinical_trials_of": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "tested_by_clinical_trials_of" }, "tested_by_preclinical_trials_of": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "tested_by_preclinical_trials_of" }, "timepoint": { @@ -2706,15 +2721,15 @@ "@id": "translation_of" }, "treated_by": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "treated_by" }, "treated_in_studies_by": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "treated_in_studies_by" }, "treatment_applications_from": { - "@type": "biolink:ChemicalOrDrugOrTreatment", + "@type": "@id", "@id": "treatment_applications_from" }, "treats": { diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld index 476439275..3893042dd 100644 --- a/project/jsonld/biolink_model.jsonld +++ b/project/jsonld/biolink_model.jsonld @@ -597,7 +597,7 @@ { "name": "chemical_formula_value", "definition_uri": "https://w3id.org/biolink/vocab/ChemicalFormulaValue", - "description": "A chemical formula", + "description": "A type of string representing a chemical formula", "notes": [ "Should be implemented as a stronger type" ], @@ -609,7 +609,7 @@ { "name": "iri_type", "definition_uri": "https://w3id.org/biolink/vocab/IriType", - "description": "An IRI", + "description": "An IRI.", "from_schema": "https://w3id.org/biolink/vocab/", "typeof": "uriorcurie", "base": "URIorCURIE", @@ -620,7 +620,7 @@ { "name": "label_type", "definition_uri": "https://w3id.org/biolink/vocab/LabelType", - "description": "A string that provides a human-readable name for an entity", + "description": "A type of string that provides a human-readable name for an entity.", "from_schema": "https://w3id.org/biolink/vocab/", "typeof": "string", "base": "str", @@ -630,7 +630,7 @@ { "name": "narrative_text", "definition_uri": "https://w3id.org/biolink/vocab/NarrativeText", - "description": "A string that provides a human-readable description of something", + "description": "A type of string that provides a human-readable description of something.", "from_schema": "https://w3id.org/biolink/vocab/", "typeof": "string", "base": "str", @@ -640,6 +640,7 @@ { "name": "symbol_type", "definition_uri": "https://w3id.org/biolink/vocab/SymbolType", + "description": "A type of string that is typically short, used as a human-readable label or symbol for an entity, such as an official gene symbol (e.g., \"BRCA1\") or a chemical symbol.", "from_schema": "https://w3id.org/biolink/vocab/", "typeof": "string", "base": "str", @@ -649,6 +650,7 @@ { "name": "frequency_value", "definition_uri": "https://w3id.org/biolink/vocab/FrequencyValue", + "description": "A quantity expressing the number of occurrences of a repeating event per unit of time (UO:0000105). Typically used for rates such as incidence or event frequency associated with a phenomenon.", "from_schema": "https://w3id.org/biolink/vocab/", "typeof": "string", "base": "str", @@ -658,6 +660,7 @@ { "name": "percentage_frequency_value", "definition_uri": "https://w3id.org/biolink/vocab/PercentageFrequencyValue", + "description": "A frequency value expressed as a percentage (UO:0000187), i.e., a dimensionless ratio multiplied by 100.", "from_schema": "https://w3id.org/biolink/vocab/", "typeof": "double", "base": "float", @@ -667,6 +670,7 @@ { "name": "quotient", "definition_uri": "https://w3id.org/biolink/vocab/Quotient", + "description": "A dimensionless value obtained by dividing one quantity by another of the same kind (UO:0010006). Used to represent ratios such as odds ratios, hazard ratios, or relative risks.", "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "ratio" @@ -682,6 +686,7 @@ "UO" ], "definition_uri": "https://w3id.org/biolink/vocab/Unit", + "description": "A standard of measurement in which the magnitude of a physical quantity is expressed (UO:0000000). Typically drawn from the Units of Measurement Ontology (UO).", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "qud:Unit" @@ -694,6 +699,7 @@ { "name": "time_type", "definition_uri": "https://w3id.org/biolink/vocab/TimeType", + "description": "A value representing a point in time, serialised as a lexical representation of xsd:time.", "from_schema": "https://w3id.org/biolink/vocab/", "typeof": "time", "base": "XSDTime", @@ -704,6 +710,7 @@ { "name": "biological_sequence", "definition_uri": "https://w3id.org/biolink/vocab/BiologicalSequence", + "description": "A string of characters representing a biological macromolecule sequence, such as a nucleic acid sequence (DNA/RNA) using the IUPAC nucleotide alphabet, or a protein sequence using the IUPAC amino-acid alphabet.", "from_schema": "https://w3id.org/biolink/vocab/", "typeof": "string", "base": "str", @@ -1157,7 +1164,7 @@ { "name": "ApprovalStatusEnum", "definition_uri": "https://w3id.org/biolink/vocab/ApprovalStatusEnum", - "description": "", + "description": "An enumeration of regulatory and development milestones for a drug or therapeutic, spanning discovery, preclinical research, FDA clinical trial phases (1-4), special review designations (e.g., fast track, breakthrough therapy, priority review), regular FDA approval, and post-approval withdrawal.", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -1224,6 +1231,7 @@ { "name": "ClinicalApprovalStatusEnum", "definition_uri": "https://w3id.org/biolink/vocab/ClinicalApprovalStatusEnum", + "description": "An enumeration describing whether a chemical or therapy is approved for use in treating a specific condition (e.g., FDA-approved for a condition, not approved, off-label use, or withdrawn following approval).", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -1252,6 +1260,7 @@ { "name": "ResearchPhaseEnum", "definition_uri": "https://w3id.org/biolink/vocab/ResearchPhaseEnum", + "description": "An enumeration of research phases describing the stage of investigation for a drug or therapy, spanning preclinical research through clinical trial phases 1 through 4 (including phase 1/2 and phase 2/3 combinations).", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -1309,6 +1318,7 @@ { "name": "DirectionQualifierEnum", "definition_uri": "https://w3id.org/biolink/vocab/DirectionQualifierEnum", + "description": "An enumeration of values that qualify a change or effect by its direction, i.e., whether the referenced quantity or activity is increased (including up-regulated) or decreased (including down-regulated).", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -1351,6 +1361,7 @@ { "name": "ChemicalEntityDerivativeEnum", "definition_uri": "https://w3id.org/biolink/vocab/ChemicalEntityDerivativeEnum", + "description": "An enumeration of relationships by which one chemical entity is derived from another, e.g., a metabolite produced from a parent compound.", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -1361,6 +1372,7 @@ { "name": "ChemicalOrGeneOrGeneProductFormOrVariantEnum", "definition_uri": "https://w3id.org/biolink/vocab/ChemicalOrGeneOrGeneProductFormOrVariantEnum", + "description": "An enumeration used as a qualifier to indicate a specific form or variant of a chemical, gene, or gene product involved in an association (e.g., modified form, loss-of-function variant, gain-of-function variant, dominant-negative variant, polymorphic form, SNP form, mutant form, or analog form).", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -1407,6 +1419,7 @@ { "name": "GeneOrGeneProductOrChemicalPartQualifierEnum", "definition_uri": "https://w3id.org/biolink/vocab/GeneOrGeneProductOrChemicalPartQualifierEnum", + "description": "An enumeration used as a qualifier to indicate a particular structural or functional part of a gene, gene product, or chemical (e.g., 3' UTR, 5' UTR, poly-A tail, promoter, enhancer, exon, or intron).", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -1435,6 +1448,7 @@ { "name": "GeneOrGeneProductOrChemicalEntityAspectEnum", "definition_uri": "https://w3id.org/biolink/vocab/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "An enumeration used as a qualifier to indicate the specific aspect of a gene, gene product, or chemical entity that is affected or measured in an association. Values cover activity and abundance (expression, synthesis, degradation, stability, localization, transport), molecular interactions, and a wide range of molecular modifications such as phosphorylation, methylation, acetylation, ubiquitination, and other post-translational or chemical modifications.", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -1654,6 +1668,7 @@ { "name": "CausalMechanismQualifierEnum", "definition_uri": "https://w3id.org/biolink/vocab/CausalMechanismQualifierEnum", + "description": "An enumeration used as a qualifier to specify the causal or pharmacologic mechanism by which an effect is exerted in an association (e.g., agonism, antagonism, inverse agonism, allosteric modulation, activation, inhibition, and their competitive or partial variants).", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -2204,6 +2219,7 @@ { "name": "LogicalInterpretationEnum", "definition_uri": "https://w3id.org/biolink/vocab/LogicalInterpretationEnum", + "description": "An enumeration of logical interpretations that can be applied to a triple to indicate whether the relation should be read as existential on both sides (some-some), universal-existential (all-some), or its inverse (inverse all-some).", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -2224,6 +2240,7 @@ { "name": "ReactionDirectionEnum", "definition_uri": "https://w3id.org/biolink/vocab/ReactionDirectionEnum", + "description": "An enumeration of possible directions for a biochemical reaction, indicating whether it proceeds left-to-right, right-to-left, is bidirectional (reversible), or has no net direction.", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -2243,6 +2260,7 @@ { "name": "ReactionSideEnum", "definition_uri": "https://w3id.org/biolink/vocab/ReactionSideEnum", + "description": "An enumeration indicating on which side of a biochemical reaction a participant appears - the left-hand (reactant/substrate) side or the right-hand (product) side, as written.", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -2313,6 +2331,7 @@ { "name": "DruggableGeneCategoryEnum", "definition_uri": "https://w3id.org/biolink/vocab/DruggableGeneCategoryEnum", + "description": "An enumeration of druggability categories for gene targets as defined by the IDG (Illuminating the Druggable Genome) / Pharos target development level classification: Tclin (targets of approved drugs), Tchem (targets with potent bioactives), Tbio (targets with biological knowledge), and Tdark (poorly characterized targets).", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -2336,7 +2355,7 @@ { "name": "DrugAvailabilityEnum", "definition_uri": "https://w3id.org/biolink/vocab/DrugAvailabilityEnum", - "description": "", + "description": "An enumeration describing how a drug or chemical entity may be obtained, distinguishing products that are available over the counter from those that require a prescription.", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -2352,6 +2371,7 @@ { "name": "DrugDeliveryEnum", "definition_uri": "https://w3id.org/biolink/vocab/DrugDeliveryEnum", + "description": "An enumeration of routes by which a drug is administered or delivered to a patient, including inhalation, oral, transdermal absorption, and various forms of injection (intravenous, subcutaneous, intramuscular).", "from_schema": "https://w3id.org/biolink/vocab/", "permissible_values": [ { @@ -2468,6 +2488,7 @@ { "name": "AgentTypeEnum", "definition_uri": "https://w3id.org/biolink/vocab/AgentTypeEnum", + "description": "An enumeration of agent types responsible for generating a statement of knowledge, as defined by the Translator Knowledge Level / Agent Type (KL/AT) standard. Values distinguish human (manual) agents from automated agents (including data analysis pipelines, computational models, text-mining agents, image-processing agents) and mixed cases such as manual validation of automated output.", "in_subset": [ "translator_minimal" ], @@ -2526,6 +2547,7 @@ { "name": "KnowledgeLevelEnum", "definition_uri": "https://w3id.org/biolink/vocab/KnowledgeLevelEnum", + "description": "An enumeration characterizing the type of knowledge expressed in a statement and the kind of evidence and reasoning that supports it, as defined by the Translator Knowledge Level / Agent Type (KL/AT) standard. Values include knowledge assertion, logical entailment, prediction, statistical association, text co-occurrence, direct observation, and not-provided.", "in_subset": [ "translator_minimal" ], @@ -2837,6 +2859,7 @@ "range": "QuantityValue", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -2969,6 +2992,7 @@ { "name": "type", "definition_uri": "https://w3id.org/biolink/vocab/type", + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "from_schema": "https://w3id.org/biolink/vocab/", "mappings": [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" @@ -3123,6 +3147,7 @@ { "name": "reaction_balanced", "definition_uri": "https://w3id.org/biolink/vocab/reaction_balanced", + "description": "Indicates whether a chemical reaction is stoichiometrically balanced, i.e. whether the conservation of atoms (and charge) holds between the reactants and the products.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "association_slot", "domain": "Association", @@ -3200,6 +3225,7 @@ { "name": "exact_synonym", "definition_uri": "https://w3id.org/biolink/vocab/exact_synonym", + "description": "An alternate label for an entity that denotes exactly the same meaning as the primary label and is interchangeable with it in all contexts.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" @@ -3215,6 +3241,7 @@ { "name": "broad_synonym", "definition_uri": "https://w3id.org/biolink/vocab/broad_synonym", + "description": "An alternate label for an entity whose meaning is broader (more general) than the primary label but is still useful as a lexical alternative.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym" @@ -3230,6 +3257,7 @@ { "name": "narrow_synonym", "definition_uri": "https://w3id.org/biolink/vocab/narrow_synonym", + "description": "An alternate label for an entity whose meaning is narrower (more specific) than the primary label, for example naming a particular sub-type.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym" @@ -3245,6 +3273,7 @@ { "name": "related_synonym", "definition_uri": "https://w3id.org/biolink/vocab/related_synonym", + "description": "An alternate label that is related to the primary label but is neither exactly synonymous nor cleanly broader or narrower; useful as a lexical pointer but not for strict equivalence. Corresponds to oboInOwl:hasRelatedSynonym.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym" @@ -3442,7 +3471,7 @@ { "name": "upstream_resource_ids", "definition_uri": "https://w3id.org/biolink/vocab/upstream_resource_ids", - "description": "An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact.", + "description": "An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "node_property", "domain": "RetrievalSource", @@ -3643,6 +3672,7 @@ { "name": "aggregate_statistic", "definition_uri": "https://w3id.org/biolink/vocab/aggregate_statistic", + "description": "An abstract grouping for summary numerical measures (e.g. count, total, quotient, percentage, rate) computed over a set of observations or a reference population, used to describe a property of an aggregated entity rather than an individual instance.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "node_property", "abstract": true, @@ -3717,6 +3747,7 @@ { "name": "has_taxonomic_rank", "definition_uri": "https://w3id.org/biolink/vocab/has_taxonomic_rank", + "description": "The taxonomic rank (e.g. species, genus, family, order, kingdom) assigned to an organism taxon.", "from_schema": "https://w3id.org/biolink/vocab/", "mappings": [ "https://www.wikidata.org/entity/P105" @@ -3734,6 +3765,7 @@ { "name": "has_dataset", "definition_uri": "https://w3id.org/biolink/vocab/has_dataset", + "description": "Links a dataset version to the underlying dataset that it is a version of.", "from_schema": "https://w3id.org/biolink/vocab/", "broad_mappings": [ "http://purl.org/dc/terms/source" @@ -3751,6 +3783,7 @@ { "name": "source_web_page", "definition_uri": "https://w3id.org/biolink/vocab/source_web_page", + "description": "A URL of a web page that documents or serves as the landing page for a data source.", "from_schema": "https://w3id.org/biolink/vocab/", "broad_mappings": [ "http://purl.org/dc/terms/source" @@ -3768,6 +3801,7 @@ { "name": "source_logo", "definition_uri": "https://w3id.org/biolink/vocab/source_logo", + "description": "A URL referencing an image that serves as the visual logo of a data source.", "from_schema": "https://w3id.org/biolink/vocab/", "mappings": [ "http://schema.org/logo" @@ -3785,6 +3819,7 @@ { "name": "retrieved_on", "definition_uri": "https://w3id.org/biolink/vocab/retrieved_on", + "description": "The date on which a dataset was retrieved or harvested from its original source, following pav:retrievedOn.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.org/pav/retrievedOn" @@ -3799,6 +3834,7 @@ { "name": "version_of", "definition_uri": "https://w3id.org/biolink/vocab/version_of", + "description": "Links a dataset version to the dataset summary of which it is a version, edition, or adaptation.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.org/dc/terms/isVersionOf" @@ -3813,6 +3849,7 @@ { "name": "version", "definition_uri": "https://w3id.org/biolink/vocab/version", + "description": "A label identifying a particular release or edition of a dataset or resource, typically following a versioning scheme such as a semantic version string or a release date.", "from_schema": "https://w3id.org/biolink/vocab/", "broad_mappings": [ "http://purl.org/pav/version", @@ -3828,6 +3865,7 @@ { "name": "license", "definition_uri": "https://w3id.org/biolink/vocab/license", + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.org/dc/terms/license" @@ -3848,6 +3886,7 @@ { "name": "rights", "definition_uri": "https://w3id.org/biolink/vocab/rights", + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.org/dc/terms/rights" @@ -3865,6 +3904,7 @@ { "name": "format", "definition_uri": "https://w3id.org/biolink/vocab/format", + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.org/dc/terms/format", @@ -3883,6 +3923,7 @@ { "name": "created_with", "definition_uri": "https://w3id.org/biolink/vocab/created_with", + "description": "An identifier (typically a URL or CURIE) of the software tool, service, or pipeline used to create the dataset.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.org/pav/createdWith" @@ -3897,6 +3938,7 @@ { "name": "download_url", "definition_uri": "https://w3id.org/biolink/vocab/download_url", + "description": "A URL from which the information content entity may be directly downloaded in its native serialization.", "from_schema": "https://w3id.org/biolink/vocab/", "mappings": [ "http://www.w3.org/ns/dcat#downloadURL" @@ -3911,6 +3953,7 @@ { "name": "dataset_download_url", "definition_uri": "https://w3id.org/biolink/vocab/dataset_download_url", + "description": "A URL from which the dataset itself may be directly downloaded specialised for the dataset domain.", "from_schema": "https://w3id.org/biolink/vocab/", "mappings": [ "http://www.w3.org/ns/dcat#downloadURL" @@ -3925,6 +3968,7 @@ { "name": "distribution_download_url", "definition_uri": "https://w3id.org/biolink/vocab/distribution_download_url", + "description": "A URL from which a specific distribution (serialization or format) of a dataset may be directly downloaded; corresponds to dcat:downloadURL specialised for the dataset distribution domain.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://www.w3.org/ns/dcat#downloadURL" @@ -3942,6 +3986,7 @@ { "name": "ingest_date", "definition_uri": "https://w3id.org/biolink/vocab/ingest_date", + "description": "The date on which a dataset version was ingested into the local knowledge graph or downstream data system; a specialization of dct:issued for the ingestion context.", "from_schema": "https://w3id.org/biolink/vocab/", "broad_mappings": [ "http://purl.org/dc/terms/issued" @@ -3959,6 +4004,7 @@ { "name": "has_distribution", "definition_uri": "https://w3id.org/biolink/vocab/has_distribution", + "description": "Links a dataset version to one of its dataset distributions (a specific representation or serialization of the dataset).", "from_schema": "https://w3id.org/biolink/vocab/", "mappings": [ "http://purl.org/dc/terms/distribution" @@ -3976,7 +4022,7 @@ { "name": "published_in", "definition_uri": "https://w3id.org/biolink/vocab/published_in", - "description": "CURIE identifier of a broader publication context within which the publication may be placed, e.g. a specified book or journal.", + "description": "CURIE identifier of a broader publication context within which the publication may be placed.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "https://www.wikidata.org/prop/P1433" @@ -4597,6 +4643,7 @@ { "name": "has_zygosity", "definition_uri": "https://w3id.org/biolink/vocab/has_zygosity", + "description": "The zygosity characterising a genotype or nucleic acid entity at a particular locus.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "node_property", "domain": "NucleicAcidEntity", @@ -4706,7 +4753,7 @@ { "name": "has_receptor", "definition_uri": "https://w3id.org/biolink/vocab/has_receptor", - "description": "the organism or organism part being exposed", + "description": "An entity that interacts with an exposure stimulus during an exposure event.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/ExO_0000001" @@ -4720,8 +4767,11 @@ }, { "name": "has_stressor", + "id_prefixes": [ + "ExO" + ], "definition_uri": "https://w3id.org/biolink/vocab/has_stressor", - "description": "the process or entity that the receptor is being exposed to", + "description": "An agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure_receptor during an exposure event.", "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "has stimulus" @@ -4832,7 +4882,7 @@ { "name": "is_supplement", "definition_uri": "https://w3id.org/biolink/vocab/is_supplement", - "description": "", + "description": "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "node_property", "domain": "ChemicalMixture", @@ -4847,7 +4897,7 @@ { "name": "trade_name", "definition_uri": "https://w3id.org/biolink/vocab/trade_name", - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "node_property", "domain": "ChemicalEntity", @@ -4862,7 +4912,13 @@ { "name": "available_from", "definition_uri": "https://w3id.org/biolink/vocab/available_from", - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", + "examples": [ + { + "value": "over_the_counter", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "node_property", "domain": "NamedThing", @@ -4878,7 +4934,7 @@ { "name": "is_toxic", "definition_uri": "https://w3id.org/biolink/vocab/is_toxic", - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "node_property", "domain": "NamedThing", @@ -4902,7 +4958,7 @@ ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "related_to_at_concept_level", - "domain": "NamedThing", + "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_chemical_role", "inherited": true, "owner": "ChemicalEntity", @@ -4920,12 +4976,12 @@ "description": "Holds between a chemical role and a chemical entity that exhibits that role.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "related_to_at_concept_level", - "domain": "NamedThing", + "domain": "ChemicalRole", "slot_uri": "https://w3id.org/biolink/vocab/is_chemical_role_of", "inherited": true, "owner": "is_chemical_role_of", "inverse": "has_chemical_role", - "range": "NamedThing", + "range": "ChemicalEntity", "multivalued": true, "@type": "SlotDefinition" }, @@ -4947,7 +5003,7 @@ { "name": "animal_model_available_from", "definition_uri": "https://w3id.org/biolink/vocab/animal_model_available_from", - "description": "", + "description": "A resource (such as a model organism database) from which an animal model representing the given disease or phenotypic feature may be obtained.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "node_property", "domain": "NamedThing", @@ -5008,7 +5064,7 @@ { "name": "FDA_adverse_event_level", "definition_uri": "https://w3id.org/biolink/vocab/FDA_adverse_event_level", - "description": "", + "description": "The level or severity grade of an adverse event as classified by FDA adverse-event terminology, drawn from FDAIDAAdverseEventEnum; used on adverse-event associations.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "association_slot", "domain": "Association", @@ -5152,12 +5208,12 @@ "examples": [ { "value": "CHEBI:5118", - "description": "In a MAXO annotation this would be a specialization in treatment of a disease. For example, fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term 'congenital myasthenic syndrome '4A.'", + "description": "fluoxetine. In a MAXO annotation this would be a specialization in treatment of a disease. For example, fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term 'congenital myasthenic syndrome '4A.'", "@type": "Example" }, { "value": "GO:0005634", - "description": "In an expression annotation this would be a specialization in location of an anatomical entity. For example, \"expression in the nucleus of hepatic cells\" would be a specialization of \"expression in hepatic cells\"", + "description": "nucleus. In an expression annotation this would be a specialization in location of an anatomical entity. For example, \"expression in the nucleus of hepatic cells\" would be a specialization of \"expression in hepatic cells\"", "@type": "Example" } ], @@ -5204,7 +5260,7 @@ "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/aspect_qualifier", "owner": "aspect_qualifier", - "range": "string", + "range": "GeneOrGeneProductOrChemicalEntityAspectEnum", "@type": "SlotDefinition" }, { @@ -5232,7 +5288,7 @@ { "name": "part_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/part_qualifier", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it).", "examples": [ { "value": "polyA tail", @@ -5261,11 +5317,8 @@ "description": "Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.", "examples": [ { - "value": "cohort x (e.g. a specific population, referenced by an identifier)", - "@type": "Example" - }, - { - "value": "gut microbiome", + "value": "OHMI:0000020", + "description": "gut microbiome", "@type": "Example" } ], @@ -5403,7 +5456,7 @@ "CausalGeneToDiseaseAssociation", "CorrelatedGeneToDiseaseAssociation" ], - "range": "string", + "range": "GeneOrGeneProductOrChemicalEntityAspectEnum", "@type": "SlotDefinition" }, { @@ -5475,7 +5528,17 @@ { "name": "subject_part_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_part_qualifier", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement).", + "examples": [ + { + "value": "polyA tail", + "@type": "Example" + }, + { + "value": "upstream control region", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -5523,6 +5586,7 @@ { "name": "subject_context_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_context_qualifier", + "description": "A qualifier describing the context in which the subject of an association holds.", "in_subset": [ "translator_minimal" ], @@ -5545,6 +5609,16 @@ "name": "subject_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -5607,7 +5681,7 @@ "EntityToFeatureOrGeneQualifiersMixin", "FeatureOrDiseaseQualifiersToEntityMixin" ], - "range": "string", + "range": "GeneOrGeneProductOrChemicalEntityAspectEnum", "@type": "SlotDefinition" }, { @@ -5675,7 +5749,17 @@ { "name": "object_part_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_part_qualifier", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement).", + "examples": [ + { + "value": "polyA tail", + "@type": "Example" + }, + { + "value": "upstream control region", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -5721,6 +5805,7 @@ { "name": "object_context_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_context_qualifier", + "description": "A qualifier describing the context in which the object of an association holds.", "in_subset": [ "translator_minimal" ], @@ -5743,6 +5828,16 @@ "name": "object_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -5778,6 +5873,13 @@ "notes": [ "to express the statement that \u201cChemical X causes increased expression of Gene Y\u201d, the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, object_direction:increased. The predicate \u2018affects\u2019 is needed for the core triple reading, but does not make sense in the full statement reading (because \u201cChemical X affects increased expression of Gene Y'' is not what we mean to say here: it causes increased expression of Gene Y)" ], + "examples": [ + { + "value": "biolink:causes", + "description": "used with `affects` predicate to express causal statements", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "qualifier", "domain": "Association", @@ -5819,7 +5921,17 @@ { "name": "causal_mechanism_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/causal_mechanism_qualifier", - "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')", + "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated", + "examples": [ + { + "value": "agonism", + "@type": "Example" + }, + { + "value": "inhibition", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -5842,15 +5954,17 @@ "definition_uri": "https://w3id.org/biolink/vocab/anatomical_context_qualifier", "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "notes": [ - "Anatomical context values can be any term from UBERON. For example, the context qualifier \u2018cerebral cortext\u2019 combines with a core concept of \u2018neuron\u2019 to express the composed concept \u2018neuron in the cerebral cortext\u2019. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." + "Anatomical context values can be any term from UBERON. For example, the context qualifier \u2018cerebral cortext\u2019 combines with a core concept of \u2018neuron\u2019 to express the composed concept \u2018neuron in the cerebral cortext\u2019. The species_context_qualifier applies taxonomic context. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." ], "examples": [ { - "value": "blood", + "value": "UBERON:0000178", + "description": "blood", "@type": "Example" }, { - "value": "cerebral cortext", + "value": "UBERON:0000956", + "description": "cerebral cortex", "@type": "Example" } ], @@ -5883,11 +5997,13 @@ ], "examples": [ { - "value": "zebrafish", + "value": "NCBITaxon:7955", + "description": "zebrafish", "@type": "Example" }, { - "value": "human", + "value": "NCBITaxon:9606", + "description": "human", "@type": "Example" } ], @@ -5918,10 +6034,12 @@ "examples": [ { "value": "MONDO:0004979", + "description": "asthma", "@type": "Example" }, { "value": "MONDO:0005148", + "description": "type 2 diabetes mellitus", "@type": "Example" } ], @@ -6102,6 +6220,7 @@ "range": "MacromolecularMachineMixin", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -6476,7 +6595,7 @@ "@type": "Annotation" } ], - "description": "a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives (e.g. drug as a type of chemical entity versus drug as a type of role borne by a chemical entity).", + "description": "a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives.", "in_subset": [ "translator_minimal" ], @@ -6879,6 +6998,7 @@ "@type": "Annotation" } ], + "description": "Holds between a gene or gene product and a cellular component in which it carries out its molecular function.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/RO_0002432" @@ -6906,6 +7026,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -6918,6 +7039,7 @@ "@type": "Annotation" } ], + "description": "Holds between a gene or gene product and a biological process such that the molecular function of the gene product, by way of a chain of causally linked events, is upstream of and contributes to the execution of the process.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/RO_0002263" @@ -6945,6 +7067,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -6957,6 +7080,7 @@ "@type": "Annotation" } ], + "description": "Holds between a gene or gene product and a biological process where the molecular function of the gene product is upstream of and has a positive (activating or increasing) effect on the execution of the process.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/RO_0004034" @@ -6984,6 +7108,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -6996,6 +7121,7 @@ "@type": "Annotation" } ], + "description": "Holds between a gene or gene product and a biological process where the molecular function of the gene product is upstream of and has a negative (inhibiting or decreasing) effect on the execution of the process.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/RO_0004035" @@ -7023,6 +7149,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -7035,6 +7162,7 @@ "@type": "Annotation" } ], + "description": "Holds between a gene or gene product and a biological process when the gene product either acts upstream of the process or participates in it; used when the more specific causal relationship is not known. Corresponds to RO:0002264.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/RO_0002264" @@ -7062,6 +7190,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -7074,6 +7203,7 @@ "@type": "Annotation" } ], + "description": "Holds between a gene or gene product and a biological process when the gene product acts upstream of or within the process with a positive (activating or increasing) effect on its execution. Corresponds to RO:0004032.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/RO_0004032" @@ -7101,6 +7231,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -7113,6 +7244,7 @@ "@type": "Annotation" } ], + "description": "Holds between a gene or gene product and a biological process when the gene product acts upstream of or within the process with a negative (inhibiting or decreasing) effect on its execution. Corresponds to RO:0004033.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/RO_0004033" @@ -7140,6 +7272,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -7181,6 +7314,7 @@ { "name": "contributor", "definition_uri": "https://w3id.org/biolink/vocab/contributor", + "description": "Links an information content entity (such as a dataset, publication, or software artefact) to an agent responsible for making contributions to it. Used as an abstract grouping predicate over more specific contribution roles (author, editor, publisher, provider). Corresponds to dct:contributor.", "comments": [ "This is a grouping for predicates relating entities to their associated contributors realizing them" ], @@ -7216,7 +7350,7 @@ { "name": "provider", "definition_uri": "https://w3id.org/biolink/vocab/provider", - "description": "person, group, organization or project that provides a piece of information (e.g. a knowledge association).", + "description": "person, group, organization or project that provides a piece of information.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "contributor", "domain": "Agent", @@ -7515,6 +7649,7 @@ "@type": "Annotation" } ], + "description": "Holds between two entities that physically interact by way of one or more intermediary entities, rather than through direct physical contact.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "physically_interacts_with", "domain": "NamedThing", @@ -7725,9 +7860,6 @@ } ], "description": "A statistical association used to indicate that the object of a statement using this predicate induces a response of some kind in the subject entity. Intentionally broad in definition, this predicate should be used with qualifiers to narrow the type of response (E.g. whether the response is therapeutic, phenotypic, detrimental, resistant, etc. is captured in context, direction, and aspect qualifiers).", - "comments": [ - "subject: NCBIGene:2064 # HER2 subject_aspect: Amplification predicate: associated with response to object: CHEBI:10035 # Trastuzumab response_type_qualifier: therapeutic_sensitivity response_direction_qualifer: increased response_target_qualifier: human patient disease_context_qualifier: MONDO:0007254 # breast cancer\nsubject: MONDO:0007254 predicate: associated with response to qualified_predicate: associated with object: CHEBI:10035 # Trastuzumab response_context_qualifier: therapeutic_sensitivity" - ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "associated_with", "domain": "NamedThing", @@ -7975,7 +8107,7 @@ "@type": "Annotation" } ], - "description": "holds between two chemical entities or genes or gene products where the action of one affects the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other.", + "description": "holds between two chemical entities or genes or gene products where the action of one affects the susceptibility/sensitivity of a biological entity or system to the other.", "in_subset": [ "translator_minimal" ], @@ -7992,6 +8124,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8010,6 +8143,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8027,7 +8161,7 @@ "@type": "Annotation" } ], - "description": "holds between two chemical entities or genes or gene products where the action or effect of one increases the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other", + "description": "holds between two chemical entities or genes or gene products where the action or effect of one increases the susceptibility/sensitivity of a biological entity or system to the other", "in_subset": [ "translator_minimal" ], @@ -8044,6 +8178,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8062,6 +8197,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8079,7 +8215,7 @@ "@type": "Annotation" } ], - "description": "holds between two chemical entities or genes or gene products where the action or effect of one decreases the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other", + "description": "holds between two chemical entities or genes or gene products where the action or effect of one decreases the susceptibility/sensitivity of a biological entity or system to the other", "in_subset": [ "translator_minimal" ], @@ -8099,6 +8235,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8117,6 +8254,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8156,6 +8294,7 @@ "range": "PhysicalEssenceOrOccurrent", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8171,6 +8310,7 @@ "range": "PhysicalEssenceOrOccurrent", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8285,6 +8425,7 @@ "range": "GeneProductMixin", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8723,6 +8864,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8755,6 +8897,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8781,6 +8924,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -8842,7 +8986,7 @@ "@type": "Annotation" } ], - "description": "", + "description": "A statistical association, observed in genetic studies, between a genetic entity such as a gene, locus, or variant and a phenotype, disease, or trait.", "in_subset": [ "translator_minimal" ], @@ -9123,6 +9267,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9178,6 +9323,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9225,6 +9371,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9274,6 +9421,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9332,6 +9480,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9426,6 +9575,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9503,6 +9653,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9521,6 +9672,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9539,6 +9691,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9616,6 +9769,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9630,7 +9784,7 @@ ], "description": "Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity was actually taken by one or more patients with the intent of treating the condition.", "notes": [ - "This predicate is used simply to report observations of use in the real world, and is agnostic to whether the treatment is approved for or might be effective in treating the condition. The treatment could be taken by a patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS where patients directly report the condition for which they took a drug, or statements from a database cataloging instances of off-label prescription of drugs for specific conditions (e.g. here, here, here)." + "This predicate is used simply to report observations of use in the real world, and is agnostic to whether the treatment is approved for or might be effective in treating the condition. The treatment could be taken by a patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS where patients directly report the condition for which they took a drug, or statements from a database cataloging instances of off-label prescription of drugs for specific conditions." ], "in_subset": [ "translator_minimal" @@ -9670,6 +9824,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9718,6 +9873,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9864,6 +10020,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9887,6 +10044,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -9981,6 +10139,7 @@ "range": "GeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -10849,6 +11008,7 @@ "range": "Occurrent", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -10861,6 +11021,7 @@ "@type": "Annotation" } ], + "description": "Holds between a macromolecular machine (typically an enzyme or ribozyme) and a biochemical reaction or process whose rate it accelerates, without itself being consumed, by lowering the activation energy.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/RO_0002327" @@ -10888,6 +11049,7 @@ "range": "Occurrent", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -10900,6 +11062,7 @@ "@type": "Annotation" } ], + "description": "Holds between a biochemical reaction or catalytic process and a chemical entity that is acted upon (consumed or transformed) by that reaction.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "has_participant", "domain": "ChemicalEntityOrGeneOrGeneProduct", @@ -10910,6 +11073,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -10925,6 +11089,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -11049,6 +11214,7 @@ "range": "Occurrent", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -11586,6 +11752,7 @@ "@type": "Annotation" } ], + "description": "Holds between a process and an entity that is taken in and depleted by the process; for example a metabolite consumed in a biochemical reaction.", "from_schema": "https://w3id.org/biolink/vocab/", "narrow_mappings": [ "http://purl.obolibrary.org/obo/RO_0004009" @@ -11654,6 +11821,7 @@ "range": "Occurrent", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -11698,6 +11866,7 @@ "range": "Occurrent", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -11728,6 +11897,7 @@ "range": "Occurrent", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -11779,6 +11949,7 @@ "@type": "Annotation" } ], + "description": "Links a genotype or genetic variant to a condition (disease or phenotypic feature) that is associated with it.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/GENO_0000790" @@ -11822,6 +11993,7 @@ "range": "GenomicEntity", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -11862,6 +12034,7 @@ "range": "GenomicEntity", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -11902,6 +12075,7 @@ "range": "GenomicEntity", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -11945,6 +12119,7 @@ "range": "GenomicEntity", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -11990,6 +12165,7 @@ "range": "GenomicEntity", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -12035,6 +12211,7 @@ "range": "GenomicEntity", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -12076,6 +12253,7 @@ "range": "GenomicEntity", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -12120,6 +12298,7 @@ "range": "GenomicEntity", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -12214,6 +12393,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -12260,6 +12440,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -12318,6 +12499,7 @@ "range": "ChemicalOrDrugOrTreatment", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -12448,6 +12630,7 @@ "@type": "Annotation" } ], + "description": "Holds between an entity and a component that is present at higher amount than in a reference state or sibling entity; used for comparative compositional statements.", "from_schema": "https://w3id.org/biolink/vocab/", "narrow_mappings": [ "http://purl.obolibrary.org/obo/CL_has_high_plasma_membrane_amount" @@ -12491,6 +12674,7 @@ "@type": "Annotation" } ], + "description": "Holds between an entity and a component that is present at lower amount than in a reference state or sibling entity; used for comparative compositional statements.", "from_schema": "https://w3id.org/biolink/vocab/", "narrow_mappings": [ "http://purl.obolibrary.org/obo/CL_has_low_plasma_membrane_amount" @@ -12534,6 +12718,7 @@ "@type": "Annotation" } ], + "description": "Holds between an entity and a component that is absent from it relative to a reference type; for example a cell type lacking a particular organelle or a protein lacking a particular domain. Corresponds to CL:lacks_part / PR:lacks_part.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/CL_lacks_part", @@ -12576,6 +12761,7 @@ "@type": "Annotation" } ], + "description": "Holds between two entities where the first develops, by one or more developmental processes, from the second; for example a cell type developing from a precursor cell type or a tissue developing from an embryonic primordium. Corresponds to RO:0002202.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "http://purl.obolibrary.org/obo/BTO_develops_from", @@ -12720,6 +12906,7 @@ "range": "ThingWithTaxon", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -13836,7 +14023,7 @@ { "name": "dataset_count", "definition_uri": "https://w3id.org/biolink/vocab/dataset_count", - "description": "The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort.", + "description": "The total number of instances in a dataset/cohort.", "examples": [ { "value": "100000", @@ -14004,7 +14191,7 @@ "description": "The segment of text from a document that supports the mined assertion.", "examples": [ { - "value": "The administration of 50g/ml bupivacaine promoted maximum breast cancer.", + "value": "Here, we report two new cases of rivaroxaban-induced hepatitis.", "@type": "Example" } ], @@ -14050,7 +14237,7 @@ "description": "Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion.", "examples": [ { - "value": "15", + "value": "33", "@type": "Example" } ], @@ -14072,7 +14259,7 @@ "description": "Character offsets for the text span(s) in the supporting text corresponding to the object concept of the extracted assertion", "examples": [ { - "value": "15", + "value": "53", "@type": "Example" } ], @@ -14094,7 +14281,7 @@ "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", "examples": [ { - "value": "15.0", + "value": "0.6188385904738642", "@type": "Example" } ], @@ -14136,7 +14323,7 @@ "description": "The document year (typically the publication year) for the supporting document used in a Text Mining Result.", "examples": [ { - "value": "1999", + "value": "2018", "@type": "Example" } ], @@ -14157,7 +14344,7 @@ "description": "The section of the supporting text of a Text Mining Result within the supporting document. This is in the form of the name of the document section (e.g., Abstract, Introduction) that contains the supporting text.", "examples": [ { - "value": "Introduction", + "value": "abstract", "@type": "Example" } ], @@ -14655,7 +14842,7 @@ { "name": "supporting_study_cohort", "definition_uri": "https://w3id.org/biolink/vocab/supporting_study_cohort", - "description": "A description of a study population/cohort that was interrogated to provide evidence for the association (e.g. the inclusion and exclusion criteria).", + "description": "A description of a study population/cohort that was interrogated to provide evidence for the association.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "supporting_study_metadata", "domain": "Association", @@ -14679,7 +14866,7 @@ { "name": "supporting_study_context", "definition_uri": "https://w3id.org/biolink/vocab/supporting_study_context", - "description": "A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue type, disease, etc.).", + "description": "A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system, tissue type, disease, etc.).", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "supporting_study_metadata", "domain": "Association", @@ -14764,7 +14951,7 @@ { "name": "has_biological_sex", "definition_uri": "https://w3id.org/biolink/vocab/has_biological_sex", - "description": "The biological sex of the entity (e.g., male or female) regarding a case description from a phenopacket", + "description": "The biological sex of the entity regarding a case description from a phenopacket", "from_schema": "https://w3id.org/biolink/vocab/", "slot_uri": "https://w3id.org/biolink/vocab/has_biological_sex", "owner": "Case", @@ -15147,6 +15334,7 @@ { "name": "organism_taxon_has_taxonomic_rank", "definition_uri": "https://w3id.org/biolink/vocab/has_taxonomic_rank", + "description": "The taxonomic rank (e.g. species, genus, family, order, kingdom) assigned to an organism taxon.", "from_schema": "https://w3id.org/biolink/vocab/", "mappings": [ "https://www.wikidata.org/entity/P105" @@ -15761,6 +15949,7 @@ "range": "MacromolecularMachineMixin", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -17059,6 +17248,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -17096,6 +17286,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -17133,6 +17324,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -17208,6 +17400,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -17351,7 +17544,7 @@ ], "is_usage_slot": true, "usage_slot_name": "subject", - "range": "Gene", + "range": "GeneFamily", "required": true, "@type": "SlotDefinition" }, @@ -17387,8 +17580,10 @@ ], "is_usage_slot": true, "usage_slot_name": "object", - "range": "GeneFamily", + "range": "GeneOrGeneProduct", "required": true, + "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -17463,6 +17658,7 @@ "range": "GeneOrGeneProductOrGeneFamily", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -17609,6 +17805,7 @@ "range": "GeneOrGeneProductOrGeneFamily", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -18119,6 +18316,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -18192,6 +18390,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -18337,6 +18536,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -18466,6 +18666,7 @@ "range": "MacromolecularMachineMixin", "multivalued": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -18650,6 +18851,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -19051,12 +19253,13 @@ ], "is_usage_slot": true, "usage_slot_name": "subject aspect qualifier", - "range": "string", + "range": "GeneOrGeneProductOrChemicalEntityAspectEnum", "@type": "SlotDefinition" }, { "name": "named_thing_associated_with_likelihood_of_named_thing_association_subject_context_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_context_qualifier", + "description": "A qualifier describing the context in which the subject of an association holds.", "in_subset": [ "translator_minimal" ], @@ -19110,12 +19313,13 @@ ], "is_usage_slot": true, "usage_slot_name": "object aspect qualifier", - "range": "string", + "range": "GeneOrGeneProductOrChemicalEntityAspectEnum", "@type": "SlotDefinition" }, { "name": "named_thing_associated_with_likelihood_of_named_thing_association_object_context_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_context_qualifier", + "description": "A qualifier describing the context in which the object of an association holds.", "in_subset": [ "translator_minimal" ], @@ -19204,6 +19408,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -19289,7 +19494,17 @@ { "name": "chemical_gene_interaction_association_subject_part_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_part_qualifier", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement).", + "examples": [ + { + "value": "polyA tail", + "@type": "Example" + }, + { + "value": "upstream control region", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -19337,6 +19552,7 @@ { "name": "chemical_gene_interaction_association_subject_context_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_context_qualifier", + "description": "A qualifier describing the context in which the subject of an association holds.", "in_subset": [ "translator_minimal" ], @@ -19358,6 +19574,16 @@ "name": "chemical_gene_interaction_association_object_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -19460,7 +19686,17 @@ { "name": "chemical_gene_interaction_association_object_part_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_part_qualifier", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement).", + "examples": [ + { + "value": "polyA tail", + "@type": "Example" + }, + { + "value": "upstream control region", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -19481,6 +19717,7 @@ { "name": "chemical_gene_interaction_association_object_context_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_context_qualifier", + "description": "A qualifier describing the context in which the object of an association holds.", "in_subset": [ "translator_minimal" ], @@ -19503,15 +19740,17 @@ "definition_uri": "https://w3id.org/biolink/vocab/anatomical_context_qualifier", "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "notes": [ - "Anatomical context values can be any term from UBERON. For example, the context qualifier \u2018cerebral cortext\u2019 combines with a core concept of \u2018neuron\u2019 to express the composed concept \u2018neuron in the cerebral cortext\u2019. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." + "Anatomical context values can be any term from UBERON. For example, the context qualifier \u2018cerebral cortext\u2019 combines with a core concept of \u2018neuron\u2019 to express the composed concept \u2018neuron in the cerebral cortext\u2019. The species_context_qualifier applies taxonomic context. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." ], "examples": [ { - "value": "blood", + "value": "UBERON:0000178", + "description": "blood", "@type": "Example" }, { - "value": "cerebral cortext", + "value": "UBERON:0000956", + "description": "cerebral cortex", "@type": "Example" } ], @@ -19536,7 +19775,17 @@ { "name": "chemical_gene_interaction_association_causal_mechanism_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/causal_mechanism_qualifier", - "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')", + "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated", + "examples": [ + { + "value": "agonism", + "@type": "Example" + }, + { + "value": "inhibition", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -19589,6 +19838,7 @@ "range": "MacromolecularMachineMixin", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -19663,6 +19913,7 @@ "range": "ChemicalEntityOrProteinOrPolypeptide", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -19697,16 +19948,14 @@ ], "is_usage_slot": true, "usage_slot_name": "subject", - "range": "GeneOrGeneProduct", + "range": "ChemicalEntityOrGeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { "name": "gene_regulates_gene_association_predicate", - "id_prefixes": [ - "regulates" - ], "definition_uri": "https://w3id.org/biolink/vocab/predicate", "local_names": { "ga4gh": { @@ -19735,6 +19984,7 @@ "domain_of": [ "GeneRegulatesGeneAssociation" ], + "subproperty_of": "regulates", "is_usage_slot": true, "usage_slot_name": "predicate", "range": "uriorcurie", @@ -19773,9 +20023,10 @@ ], "is_usage_slot": true, "usage_slot_name": "object", - "range": "GeneOrGeneProduct", + "range": "ChemicalEntityOrGeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -19822,6 +20073,16 @@ "name": "gene_regulates_gene_association_object_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -19847,6 +20108,13 @@ "notes": [ "to express the statement that \u201cChemical X causes increased expression of Gene Y\u201d, the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, object_direction:increased. The predicate \u2018affects\u2019 is needed for the core triple reading, but does not make sense in the full statement reading (because \u201cChemical X affects increased expression of Gene Y'' is not what we mean to say here: it causes increased expression of Gene Y)" ], + "examples": [ + { + "value": "biolink:causes", + "description": "used with `affects` predicate to express causal statements", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "qualified_predicate", "domain": "GeneRegulatesGeneAssociation", @@ -20054,7 +20322,17 @@ { "name": "chemical_affects_biological_entity_association_subject_part_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_part_qualifier", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement).", + "examples": [ + { + "value": "polyA tail", + "@type": "Example" + }, + { + "value": "upstream control region", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -20141,6 +20419,7 @@ { "name": "chemical_affects_biological_entity_association_subject_context_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_context_qualifier", + "description": "A qualifier describing the context in which the subject of an association holds.", "in_subset": [ "translator_minimal" ], @@ -20162,6 +20441,16 @@ "name": "chemical_affects_biological_entity_association_subject_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -20223,6 +20512,13 @@ "notes": [ "to express the statement that \u201cChemical X causes increased expression of Gene Y\u201d, the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, object_direction:increased. The predicate \u2018affects\u2019 is needed for the core triple reading, but does not make sense in the full statement reading (because \u201cChemical X affects increased expression of Gene Y'' is not what we mean to say here: it causes increased expression of Gene Y)" ], + "examples": [ + { + "value": "biolink:causes", + "description": "used with `affects` predicate to express causal statements", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "qualified_predicate", "domain": "ChemicalAffectsBiologicalEntityAssociation", @@ -20320,7 +20616,17 @@ { "name": "chemical_affects_biological_entity_association_object_part_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_part_qualifier", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement).", + "examples": [ + { + "value": "polyA tail", + "@type": "Example" + }, + { + "value": "upstream control region", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -20380,6 +20686,7 @@ { "name": "chemical_affects_biological_entity_association_object_context_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_context_qualifier", + "description": "A qualifier describing the context in which the object of an association holds.", "in_subset": [ "translator_minimal" ], @@ -20401,6 +20708,16 @@ "name": "chemical_affects_biological_entity_association_object_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -20421,7 +20738,17 @@ { "name": "chemical_affects_biological_entity_association_causal_mechanism_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/causal_mechanism_qualifier", - "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')", + "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated", + "examples": [ + { + "value": "agonism", + "@type": "Example" + }, + { + "value": "inhibition", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -20444,15 +20771,17 @@ "definition_uri": "https://w3id.org/biolink/vocab/anatomical_context_qualifier", "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "notes": [ - "Anatomical context values can be any term from UBERON. For example, the context qualifier \u2018cerebral cortext\u2019 combines with a core concept of \u2018neuron\u2019 to express the composed concept \u2018neuron in the cerebral cortext\u2019. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." + "Anatomical context values can be any term from UBERON. For example, the context qualifier \u2018cerebral cortext\u2019 combines with a core concept of \u2018neuron\u2019 to express the composed concept \u2018neuron in the cerebral cortext\u2019. The species_context_qualifier applies taxonomic context. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." ], "examples": [ { - "value": "blood", + "value": "UBERON:0000178", + "description": "blood", "@type": "Example" }, { - "value": "cerebral cortext", + "value": "UBERON:0000956", + "description": "cerebral cortex", "@type": "Example" } ], @@ -20483,11 +20812,13 @@ ], "examples": [ { - "value": "zebrafish", + "value": "NCBITaxon:7955", + "description": "zebrafish", "@type": "Example" }, { - "value": "human", + "value": "NCBITaxon:9606", + "description": "human", "@type": "Example" } ], @@ -20540,9 +20871,10 @@ ], "is_usage_slot": true, "usage_slot_name": "subject", - "range": "GeneOrGeneProduct", + "range": "ChemicalEntityOrGeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -20591,7 +20923,17 @@ { "name": "gene_affects_chemical_association_subject_part_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_part_qualifier", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement).", + "examples": [ + { + "value": "polyA tail", + "@type": "Example" + }, + { + "value": "upstream control region", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -20651,6 +20993,7 @@ { "name": "gene_affects_chemical_association_subject_context_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_context_qualifier", + "description": "A qualifier describing the context in which the subject of an association holds.", "in_subset": [ "translator_minimal" ], @@ -20672,6 +21015,16 @@ "name": "gene_affects_chemical_association_subject_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -20733,6 +21086,13 @@ "notes": [ "to express the statement that \u201cChemical X causes increased expression of Gene Y\u201d, the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, object_direction:increased. The predicate \u2018affects\u2019 is needed for the core triple reading, but does not make sense in the full statement reading (because \u201cChemical X affects increased expression of Gene Y'' is not what we mean to say here: it causes increased expression of Gene Y)" ], + "examples": [ + { + "value": "biolink:causes", + "description": "used with `affects` predicate to express causal statements", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "qualified_predicate", "domain": "GeneAffectsChemicalAssociation", @@ -20830,7 +21190,17 @@ { "name": "gene_affects_chemical_association_object_part_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_part_qualifier", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement).", + "examples": [ + { + "value": "polyA tail", + "@type": "Example" + }, + { + "value": "upstream control region", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -20917,6 +21287,7 @@ { "name": "gene_affects_chemical_association_object_context_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_context_qualifier", + "description": "A qualifier describing the context in which the object of an association holds.", "in_subset": [ "translator_minimal" ], @@ -20938,6 +21309,16 @@ "name": "gene_affects_chemical_association_object_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -20958,7 +21339,17 @@ { "name": "gene_affects_chemical_association_causal_mechanism_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/causal_mechanism_qualifier", - "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')", + "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated", + "examples": [ + { + "value": "agonism", + "@type": "Example" + }, + { + "value": "inhibition", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -20981,15 +21372,17 @@ "definition_uri": "https://w3id.org/biolink/vocab/anatomical_context_qualifier", "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", "notes": [ - "Anatomical context values can be any term from UBERON. For example, the context qualifier \u2018cerebral cortext\u2019 combines with a core concept of \u2018neuron\u2019 to express the composed concept \u2018neuron in the cerebral cortext\u2019. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." + "Anatomical context values can be any term from UBERON. For example, the context qualifier \u2018cerebral cortext\u2019 combines with a core concept of \u2018neuron\u2019 to express the composed concept \u2018neuron in the cerebral cortext\u2019. The species_context_qualifier applies taxonomic context. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." ], "examples": [ { - "value": "blood", + "value": "UBERON:0000178", + "description": "blood", "@type": "Example" }, { - "value": "cerebral cortext", + "value": "UBERON:0000956", + "description": "cerebral cortex", "@type": "Example" } ], @@ -21020,11 +21413,13 @@ ], "examples": [ { - "value": "zebrafish", + "value": "NCBITaxon:7955", + "description": "zebrafish", "@type": "Example" }, { - "value": "human", + "value": "NCBITaxon:9606", + "description": "human", "@type": "Example" } ], @@ -21080,6 +21475,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -21348,6 +21744,7 @@ "range": "Outcome", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -22131,6 +22528,7 @@ { "name": "case_to_variant_association_has_zygosity", "definition_uri": "https://w3id.org/biolink/vocab/has_zygosity", + "description": "The zygosity characterising a genotype or nucleic acid entity at a particular locus.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "has_zygosity", "domain": "CaseToVariantAssociation", @@ -22180,6 +22578,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -22289,6 +22688,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -22381,6 +22781,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -22505,6 +22906,16 @@ "name": "gene_to_phenotypic_feature_association_object_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -22593,6 +23004,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -22681,6 +23093,16 @@ "name": "gene_to_disease_association_object_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -22805,6 +23227,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -22878,6 +23301,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -22988,6 +23412,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -23828,6 +24253,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -24153,6 +24579,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -24263,6 +24690,7 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -24512,6 +24940,7 @@ "range": "MacromolecularMachineMixin", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -25272,6 +25701,7 @@ "range": "GeneProductMixin", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -25456,6 +25886,7 @@ "range": "ChemicalEntityOrGeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -25494,12 +25925,23 @@ "range": "GeneOrGeneProduct", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { "name": "chemical_entity_or_gene_or_gene_product_regulates_gene_association_object_direction_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_direction_qualifier", "description": "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).", + "examples": [ + { + "value": "increased", + "@type": "Example" + }, + { + "value": "downregulated", + "@type": "Example" + } + ], "in_subset": [ "translator_minimal" ], @@ -25951,6 +26393,7 @@ "range": "GeneOrGeneProductOrGeneFamily", "required": true, "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -26524,7 +26967,7 @@ { "name": "KnowledgeGraph", "definition_uri": "https://w3id.org/biolink/vocab/KnowledgeGraph", - "description": "A knowledge graph represented in KGX format", + "description": "A container representing a knowledge graph serialized in KGX (Knowledge Graph Exchange) format. A KnowledgeGraph aggregates a collection of nodes (entities) and edges (relationships between entities) conforming to the KGX specification, enabling interoperable exchange of biomedical knowledge graphs across tools and systems in the Biolink ecosystem.", "from_schema": "https://w3id.org/biolink/vocab/", "slots": [ "nodes", @@ -26537,7 +26980,7 @@ { "name": "Node", "definition_uri": "https://w3id.org/biolink/vocab/Node", - "description": "A node in a KGX graph, will be superclass for named thing", + "description": "A generic node in a KGX-formatted knowledge graph, representing a single entity or concept with a unique identifier. This class serves as the structural superclass for `named thing` in Biolink, providing the minimal KGX-compliant contract (identifier, category, etc.) that any biolink entity participating in a knowledge graph must satisfy.", "from_schema": "https://w3id.org/biolink/vocab/", "slot_usage": {}, "class_uri": "https://w3id.org/biolink/vocab/Node", @@ -26546,7 +26989,7 @@ { "name": "Edge", "definition_uri": "https://w3id.org/biolink/vocab/Edge", - "description": "An edge in a KGX graph, will be superclass for association", + "description": "A generic edge in a KGX-formatted knowledge graph, representing a directed relationship between a subject node and an object node qualified by a predicate. This class serves as the structural superclass for `association` in Biolink, providing the minimal KGX-compliant contract (subject, predicate, object, and associated metadata) that any biolink relationship participating in a knowledge graph must satisfy.", "from_schema": "https://w3id.org/biolink/vocab/", "slot_usage": {}, "class_uri": "https://w3id.org/biolink/vocab/Edge", @@ -26570,7 +27013,7 @@ { "name": "MappingCollection", "definition_uri": "https://w3id.org/biolink/vocab/MappingCollection", - "description": "A collection of deprecated mappings.", + "description": "An abstract container class that holds a set of predicate mappings. Serves as a top-level root for documents that enumerate how third-party or deprecated predicates should be rewritten to Biolink predicates and their associated qualifiers.", "from_schema": "https://w3id.org/biolink/vocab/", "abstract": true, "slots": [ @@ -26728,6 +27171,7 @@ "examples": [ { "value": "CHEBI:35469", + "description": "antidepressant role", "@type": "Example" } ], @@ -26763,6 +27207,7 @@ { "name": "BiologicalSex", "definition_uri": "https://w3id.org/biolink/vocab/BiologicalSex", + "description": "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "PATO:0000047" @@ -26892,6 +27337,7 @@ { "name": "RelationshipQuantifier", "definition_uri": "https://w3id.org/biolink/vocab/RelationshipQuantifier", + "description": "A mixin for quantifying aspects of the strength, frequency, or specificity of a relationship between two entities.", "from_schema": "https://w3id.org/biolink/vocab/", "mixin": true, "slot_usage": {}, @@ -26901,6 +27347,7 @@ { "name": "SensitivityQuantifier", "definition_uri": "https://w3id.org/biolink/vocab/SensitivityQuantifier", + "description": "A relationship quantifier that measures the sensitivity of a relationship, such as the proportion of true positives correctly identified in a diagnostic or association context.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "RelationshipQuantifier", "mixin": true, @@ -26911,6 +27358,7 @@ { "name": "SpecificityQuantifier", "definition_uri": "https://w3id.org/biolink/vocab/SpecificityQuantifier", + "description": "A relationship quantifier that measures the specificity of a relationship, such as the proportion of true negatives correctly identified in a diagnostic or association context.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "RelationshipQuantifier", "mixin": true, @@ -26932,6 +27380,18 @@ { "name": "FrequencyQuantifier", "definition_uri": "https://w3id.org/biolink/vocab/FrequencyQuantifier", + "description": "A relationship quantifier that expresses how often a relationship holds, using count, total, quotient, or percentage measures.", + "examples": [ + { + "object": { + "has_count": 42, + "has_total": 100, + "has_quotient": 0.42, + "has_percentage": 42.0 + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "RelationshipQuantifier", "mixin": true, @@ -26954,6 +27414,7 @@ "MAXO" ], "definition_uri": "https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatment", + "description": "A mixin for entities that represent chemical substances, pharmacological agents, or therapeutic interventions.", "from_schema": "https://w3id.org/biolink/vocab/", "mixin": true, "slot_usage": {}, @@ -27131,6 +27592,7 @@ { "name": "AdministrativeEntity", "definition_uri": "https://w3id.org/biolink/vocab/AdministrativeEntity", + "description": "An entity that is the byproduct of an administrative process.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "NamedThing", "abstract": true, @@ -27325,6 +27787,29 @@ "name": "TextMiningStudyResult", "definition_uri": "https://w3id.org/biolink/vocab/TextMiningStudyResult", "description": "A study result that represents information extracted from text using natural language processing techniques. This includes the extracted text, location offsets within the source document, confidence scores, and other metadata related to the text mining process.", + "examples": [ + { + "object": { + "id": "tmkp:id", + "category": "biolink:TextMiningStudyResult", + "supporting_text": [ + "Here, we report two new cases of rivaroxaban-induced hepatitis." + ], + "subject_location_in_text": [ + 33, + 44 + ], + "object_location_in_text": [ + 53, + 62 + ], + "extraction_confidence_score": 0.6188385904738642, + "supporting_document_year": 2018, + "supporting_text_section_type": "abstract" + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "StudyResult", "slots": [ @@ -27868,7 +28353,7 @@ "NLMID" ], "definition_uri": "https://w3id.org/biolink/vocab/Publication", - "description": "Any \u2018published\u2019 piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP).", + "description": "Any \u2018published\u2019 piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope.", "in_subset": [ "model_organism_database" ], @@ -27959,6 +28444,7 @@ { "name": "BookChapter", "definition_uri": "https://w3id.org/biolink/vocab/BookChapter", + "description": "A section of a book that forms a discrete unit of a larger published work and may be independently authored or cited.", "in_subset": [ "model_organism_database" ], @@ -28318,6 +28804,20 @@ "name": "RetrievalSource", "definition_uri": "https://w3id.org/biolink/vocab/RetrievalSource", "description": "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.", + "examples": [ + { + "object": { + "id": "urn:uuid:id", + "category": "biolink:RetrievalSource", + "resource_id": "infores:text-mining-provider-targeted", + "resource_role": "primary_knowledge_source", + "upstream_resource_ids": [ + "infores:pubmed" + ] + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "InformationContentEntity", "slots": [ @@ -28481,7 +28981,8 @@ { "name": "Procedure", "id_prefixes": [ - "CPT" + "CPT", + "MAXO" ], "definition_uri": "https://w3id.org/biolink/vocab/Procedure", "description": "A series of actions conducted in a certain order or manner", @@ -28494,7 +28995,8 @@ "STY:T059", "STY:T060", "STY:T061", - "STY:T063" + "STY:T063", + "MAXO:0000001" ], "is_a": "NamedThing", "mixins": [ @@ -28744,6 +29246,7 @@ { "name": "EnvironmentalProcess", "definition_uri": "https://w3id.org/biolink/vocab/EnvironmentalProcess", + "description": "A process that occurs within or involves the components of an environmental system.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "ENVO:02500000" @@ -28776,6 +29279,7 @@ { "name": "EnvironmentalFeature", "definition_uri": "https://w3id.org/biolink/vocab/EnvironmentalFeature", + "description": "A system or entity in the natural environment that has the disposition to environ one or more material entities.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "ENVO:01000254" @@ -28882,6 +29386,7 @@ { "name": "BiologicalEntity", "definition_uri": "https://w3id.org/biolink/vocab/BiologicalEntity", + "description": "A heterogeneous substance that contains genomic material or is the product of a biological process.", "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "bioentity" @@ -28923,6 +29428,7 @@ { "name": "GenomicEntity", "definition_uri": "https://w3id.org/biolink/vocab/GenomicEntity", + "description": "A generically dependent continuant that carries biological sequence that is part of or derived from a genome.", "in_subset": [ "translator_minimal" ], @@ -28942,6 +29448,7 @@ { "name": "EpigenomicEntity", "definition_uri": "https://w3id.org/biolink/vocab/EpigenomicEntity", + "description": "A mixin for entities that represent epigenomic modifications or features associated with heritable changes in gene expression that do not involve changes to the DNA sequence itself.", "in_subset": [ "translator_minimal" ], @@ -29846,6 +30353,7 @@ "ncats.bioplanet" ], "definition_uri": "https://w3id.org/biolink/vocab/Pathway", + "description": "A hierarchical ordering of connected molecular reactions (steps) that represent a specific biological process, such as signaling or metabolism.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "PW:0000001", @@ -29892,6 +30400,7 @@ "REACT" ], "definition_uri": "https://w3id.org/biolink/vocab/PhysiologicalProcess", + "description": "A biological or chemical function within a living organism.", "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "physiology" @@ -29939,6 +30448,7 @@ { "name": "Behavior", "definition_uri": "https://w3id.org/biolink/vocab/Behavior", + "description": "The internally coordinated responses (actions or inactions) of organisms (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "GO:0007610", @@ -30172,7 +30682,11 @@ "UMLS" ], "definition_uri": "https://w3id.org/biolink/vocab/EnvironmentalFoodContaminant", + "description": "Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate foodstuffs during their production, transportation or storage.", "from_schema": "https://w3id.org/biolink/vocab/", + "exact_mappings": [ + "CHEBI:78299" + ], "related_mappings": [ "CHEBI:78299" ], @@ -30240,7 +30754,11 @@ "UMLS" ], "definition_uri": "https://w3id.org/biolink/vocab/FoodAdditive", + "description": "Any substance which is added to food to preserve or enhance its flavour and/or appearance.", "from_schema": "https://w3id.org/biolink/vocab/", + "exact_mappings": [ + "CHEBI:64047" + ], "related_mappings": [ "CHEBI:64047" ], @@ -30309,8 +30827,12 @@ "UMLS" ], "definition_uri": "https://w3id.org/biolink/vocab/Food", - "description": "A substance consumed by a living organism as a source of nutrition", + "description": "A substance of plant, animal, or artificial origin consumed by a living organism to provide essential nutrients, energy, and support growth and the processes of life, or to satisfy other health needs or provide a social or organoleptic experience.", "from_schema": "https://w3id.org/biolink/vocab/", + "exact_mappings": [ + "CHEBI:33290", + "FOODON:00002403" + ], "is_a": "ChemicalMixture", "slots": [ "id", @@ -30384,10 +30906,10 @@ { "name": "PhenotypicQuality", "definition_uri": "https://w3id.org/biolink/vocab/PhenotypicQuality", - "description": "A property of a phenotype", + "description": "A characteristic of a phenotype (e.g., weight, size, shape, color) that can be observed, measured, or compared across organisms or conditions.", "examples": [ { - "value": "weight", + "value": "PATO:0000128", "@type": "Example" } ], @@ -30395,8 +30917,8 @@ "aliases": [ "phenotypic properties" ], - "mappings": [ - "PATO:0000001" + "broad_mappings": [ + "PATO:0001995" ], "is_a": "OrganismAttribute", "slots": [ @@ -30431,7 +30953,7 @@ "NCIT" ], "definition_uri": "https://w3id.org/biolink/vocab/GeneticInheritance", - "description": "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.", + "description": "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next.", "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "inheritance" @@ -30546,6 +31068,9 @@ "name": "Virus", "definition_uri": "https://w3id.org/biolink/vocab/Virus", "description": "A virus is a microorganism that replicates itself as a microRNA and infects the host cell.", + "comments": [ + "see: https://github.com/OBOFoundry/COB/pull/211" + ], "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "NCBITaxon:10239", @@ -30581,7 +31106,10 @@ { "name": "CellularOrganism", "definition_uri": "https://w3id.org/biolink/vocab/CellularOrganism", - "description": "", + "description": "An organism that contains one or more cells belonging to the cellular lineages of life (Archaea, Bacteria, or Eukaryota), whose body consists of one or more cells. Distinguished from acellular biological entities such as viruses and viroids.", + "comments": [ + "see: https://github.com/OBOFoundry/COB/pull/211" + ], "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "NCBITaxon:131567" @@ -30616,7 +31144,7 @@ { "name": "Mammal", "definition_uri": "https://w3id.org/biolink/vocab/Mammal", - "description": "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex", + "deprecated": "True", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "NCBITaxon:40674", @@ -30654,7 +31182,7 @@ { "name": "Human", "definition_uri": "https://w3id.org/biolink/vocab/Human", - "description": "A member of the the species Homo sapiens.", + "deprecated": "True", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "STY:T016", @@ -30692,7 +31220,7 @@ { "name": "Plant", "definition_uri": "https://w3id.org/biolink/vocab/Plant", - "description": "", + "deprecated": "True", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "NCIT:C14258", @@ -30727,7 +31255,7 @@ { "name": "Invertebrate", "definition_uri": "https://w3id.org/biolink/vocab/Invertebrate", - "description": "An animal lacking a vertebral column. This group consists of 98% of all animal species.", + "deprecated": "True", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "NCIT:C14228", @@ -30765,7 +31293,7 @@ { "name": "Vertebrate", "definition_uri": "https://w3id.org/biolink/vocab/Vertebrate", - "description": "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column.", + "deprecated": "True", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "STY:T010", @@ -30802,7 +31330,7 @@ { "name": "Fungus", "definition_uri": "https://w3id.org/biolink/vocab/Fungus", - "description": "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds).", + "deprecated": "True", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "STY:T004", @@ -30892,7 +31420,13 @@ "ORCID" ], "definition_uri": "https://w3id.org/biolink/vocab/IndividualOrganism", - "description": "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576", + "description": "An instance of an organism. For example, Charles Darwin, my pet cat.", + "examples": [ + { + "value": "ORCID:0000-0002-5355-2576", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "organism" @@ -30986,12 +31520,12 @@ { "name": "DiseaseOrPhenotypicFeature", "definition_uri": "https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature", - "description": "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature.", + "description": "A disease or an individual phenotypic feature, grouped as a single class to accommodate source vocabularies and assertions that do not distinguish the two. Prefer the more specific subclasses disease or phenotypic feature when the distinction is known.", "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "phenome" ], - "narrow_mappings": [ + "related_mappings": [ "STY:T033" ], "is_a": "BiologicalEntity", @@ -31047,7 +31581,7 @@ "PHARMGKB.DISEASE" ], "definition_uri": "https://w3id.org/biolink/vocab/Disease", - "description": "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.", + "description": "A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury.", "in_subset": [ "model_organism_database", "translator_minimal" @@ -31122,7 +31656,7 @@ "TO" ], "definition_uri": "https://w3id.org/biolink/vocab/PhenotypicFeature", - "description": "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.", + "description": "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual often resulting from the interaction of its genotype with its molecular and physical environment.", "examples": [ { "value": "MP:0001262", @@ -31243,7 +31777,19 @@ "FMA" ], "definition_uri": "https://w3id.org/biolink/vocab/AnatomicalEntity", - "description": "A subcellular location, cell type or gross anatomical part", + "description": "A part of a cellular organism at or above the granularity of a protein complex. This is a grouping class with three concrete subclasses that should be preferred when applicable: \"biolink:Cell\" for whole cells, \"biolink:CellularComponent\" for subcellular and intracellular structures (organelles, membranes, bacterial flagella, etc.), and \"biolink:GrossAnatomcialStructure\" for multicellular parts (tissues, organs, body parts). Excludes viral and other acellular biological entities.", + "examples": [ + { + "value": "UBERON:0000178", + "description": "blood", + "@type": "Example" + }, + { + "value": "UBERON:0002553", + "description": "anatomical cavity", + "@type": "Example" + } + ], "in_subset": [ "model_organism_database" ], @@ -31314,6 +31860,33 @@ ], "definition_uri": "https://w3id.org/biolink/vocab/CellularComponent", "description": "A location in or around a cell", + "examples": [ + { + "value": "GO:0005739", + "description": "mitochondrion", + "@type": "Example" + }, + { + "value": "GO:0005634", + "description": "nucleus", + "@type": "Example" + }, + { + "value": "GO:0005886", + "description": "plasma membrane", + "@type": "Example" + }, + { + "value": "GO:0009288", + "description": "bacterial-type flagellum", + "@type": "Example" + }, + { + "value": "GO:0031012", + "description": "extracellular matrix", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "cell component", @@ -31365,6 +31938,19 @@ "MESH" ], "definition_uri": "https://w3id.org/biolink/vocab/Cell", + "description": "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.", + "examples": [ + { + "value": "CL:0000540", + "description": "neuron", + "@type": "Example" + }, + { + "value": "CL:0000236", + "description": "B cell", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "GO:0005623", @@ -31404,6 +31990,7 @@ "CLO" ], "definition_uri": "https://w3id.org/biolink/vocab/CellLine", + "description": "A cultured cell population that is genetically stable and homogeneous, sharing a common propagation history through successive passages in culture.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "CLO:0000031" @@ -31446,6 +32033,39 @@ "FAO" ], "definition_uri": "https://w3id.org/biolink/vocab/GrossAnatomicalStructure", + "description": "An anatomical structure that has more than one cell as a part.", + "examples": [ + { + "value": "UBERON:0000955", + "description": "brain", + "@type": "Example" + }, + { + "value": "UBERON:0002107", + "description": "liver", + "@type": "Example" + }, + { + "value": "UBERON:0000479", + "description": "tissue", + "@type": "Example" + }, + { + "value": "PO:0009046", + "description": "flower", + "@type": "Example" + }, + { + "value": "PO:0009025", + "description": "leaf", + "@type": "Example" + }, + { + "value": "FAO:0001001", + "description": "hypha", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "tissue", @@ -31541,9 +32161,13 @@ { "name": "GeneOrGeneProductOrGeneFamily", "definition_uri": "https://w3id.org/biolink/vocab/GeneOrGeneProductOrGeneFamily", - "description": "A union of gene family or gene loci or gene products, useful to define the association between a gene or gene product or gene family and some other general class of entity (e.g. biological process or anatomical entity)", + "description": "A union of gene family or gene loci or gene products, useful to define the association between a gene or gene product or gene family and some other general class of entity.", "from_schema": "https://w3id.org/biolink/vocab/", + "is_a": "MacromolecularMachineMixin", "mixin": true, + "slots": [ + "macromolecular_machine_mixin_name" + ], "slot_usage": {}, "class_uri": "https://w3id.org/biolink/vocab/GeneOrGeneProductOrGeneFamily", "@type": "ClassDefinition" @@ -31592,6 +32216,7 @@ "is_a": "BiologicalEntity", "mixins": [ "GeneOrGeneProduct", + "GeneOrGeneProductOrGeneFamily", "GenomicEntity", "ChemicalEntityOrGeneOrGeneProduct", "PhysicalEssence", @@ -31714,7 +32339,7 @@ { "name": "NucleosomeModification", "definition_uri": "https://w3id.org/biolink/vocab/NucleosomeModification", - "description": "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.", + "description": "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "BiologicalEntity", "mixins": [ @@ -31871,6 +32496,7 @@ { "name": "CodingSequence", "definition_uri": "https://w3id.org/biolink/vocab/CodingSequence", + "description": "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "SO:0000316", @@ -32017,7 +32643,10 @@ "ENSEMBL" ], "definition_uri": "https://w3id.org/biolink/vocab/ProteinIsoform", - "description": "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/", + "description": "Represents a protein that is a specific isoform of the canonical or reference protein.", + "comments": [ + "See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" + ], "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "proteoform" @@ -32052,7 +32681,7 @@ { "name": "ProteinDomain", "definition_uri": "https://w3id.org/biolink/vocab/ProteinDomain", - "description": "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.", + "description": "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "NCIT:C13379", @@ -32090,9 +32719,28 @@ }, { "name": "PosttranslationalModification", + "id_prefixes": [ + "MOD", + "UNIMOD" + ], "definition_uri": "https://w3id.org/biolink/vocab/PosttranslationalModification", - "description": "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination.", + "description": "A chemical modification of a polypeptide or protein that occurs after translation, altering its structure, activity, localization, or interactions.", + "examples": [ + { + "value": "MOD:00696", + "description": "phosphorylated residue", + "@type": "Example" + }, + { + "value": "MOD:01148", + "description": "ubiquitinylated lysine", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", + "exact_mappings": [ + "MOD:00000" + ], "is_a": "BiologicalEntity", "mixins": [ "GeneProductIsoformMixin" @@ -32123,6 +32771,7 @@ { "name": "ProteinFamily", "definition_uri": "https://w3id.org/biolink/vocab/ProteinFamily", + "description": "A set of proteins coding for diverse functions which, by virtue of their high degree of sequence similarity, are believed to have evolved from a single ancestral gene.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "NCIT:C26004", @@ -32165,7 +32814,7 @@ { "name": "NucleicAcidSequenceMotif", "definition_uri": "https://w3id.org/biolink/vocab/NucleicAcidSequenceMotif", - "description": "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences.", + "description": "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. consensus sequences.", "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "consensus sequence" @@ -32197,9 +32846,21 @@ { "name": "RNAProduct", "id_prefixes": [ - "RNACENTRAL" + "RNACENTRAL", + "mirbase" ], "definition_uri": "https://w3id.org/biolink/vocab/RNAProduct", + "description": "High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds typically synthesized by a DNA- or RNA-dependent RNA polymerase that constitutes the product of a gene. Distinct in emphasis from `biolink:Transcript`, which denotes the informational output of transcription at the gene-model level rather than the chemical species itself.", + "examples": [ + { + "value": "RNACENTRAL:URS00005EB5B7_9606", + "@type": "Example" + }, + { + "value": "mirbase:MI0000060", + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "CHEBI:33697", @@ -32275,6 +32936,7 @@ "ENSEMBL" ], "definition_uri": "https://w3id.org/biolink/vocab/NoncodingRNAProduct", + "description": "An RNA transcript that does not encode for a protein rather the RNA molecule is the functional gene product.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "SO:0000655", @@ -32309,9 +32971,11 @@ "id_prefixes": [ "MIR", "HGNC", - "WormBase" + "WormBase", + "mirbase" ], "definition_uri": "https://w3id.org/biolink/vocab/MicroRNA", + "description": "A small (~22 nucleotide) RNA molecule that is the endogenous transcript of a miRNA gene. Produced from precursor molecules that form hairpin structures, which are processed (typically via the Dicer pathway) to yield a single miRNA molecule. miRNAs function by triggering cleavage of target molecules or acting as translational repressors.", "in_subset": [ "model_organism_database" ], @@ -32449,6 +33113,7 @@ "is_a": "BiologicalEntity", "mixins": [ "GeneGroupingMixin", + "GeneOrGeneProductOrGeneFamily", "ChemicalEntityOrGeneOrGeneProduct" ], "slots": [ @@ -32478,6 +33143,7 @@ { "name": "Zygosity", "definition_uri": "https://w3id.org/biolink/vocab/Zygosity", + "description": "An allelic state describing the degree of similarity between features at a single locus, specifically whether alleles at the same location on paired chromosomes are identical or different.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "GENO:0000133" @@ -33016,6 +33682,7 @@ { "name": "ClinicalIntervention", "definition_uri": "https://w3id.org/biolink/vocab/ClinicalIntervention", + "description": "A medical procedure, treatment, or action taken by healthcare professionals to modify the course of a disease or condition.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "ClinicalEntity", "slots": [ @@ -33077,6 +33744,7 @@ { "name": "Hospitalization", "definition_uri": "https://w3id.org/biolink/vocab/Hospitalization", + "description": "The admission and care of a patient in a hospital for observation, diagnosis, or treatment.", "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "SNOMEDCT:32485007", @@ -33373,7 +34041,7 @@ { "name": "PathologicalProcessExposure", "definition_uri": "https://w3id.org/biolink/vocab/PathologicalProcessExposure", - "description": "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease.", + "description": "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "ExposureEvent", "slots": [ @@ -33444,7 +34112,7 @@ { "name": "PathologicalAnatomicalExposure", "definition_uri": "https://w3id.org/biolink/vocab/PathologicalAnatomicalExposure", - "description": "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome.", + "description": "An abnormal anatomical structure, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "ExposureEvent", "slots": [ @@ -33480,7 +34148,7 @@ { "name": "DiseaseOrPhenotypicFeatureExposure", "definition_uri": "https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureExposure", - "description": "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer.", + "description": "A disease or phenotypic feature state, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome,.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "ExposureEvent", "mixins": [ @@ -33560,7 +34228,7 @@ { "name": "ComplexChemicalExposure", "definition_uri": "https://w3id.org/biolink/vocab/ComplexChemicalExposure", - "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.", + "description": "A complex chemical exposure is an intake of a chemical mixture, other than a drug.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "ExposureEvent", "slots": [ @@ -33905,7 +34573,7 @@ { "name": "SocioeconomicExposure", "definition_uri": "https://w3id.org/biolink/vocab/SocioeconomicExposure", - "description": "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty).", + "description": "A socioeconomic exposure is a factor relating to social and financial status of an affected individual.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "ExposureEvent", "slots": [ @@ -33941,7 +34609,7 @@ { "name": "Outcome", "definition_uri": "https://w3id.org/biolink/vocab/Outcome", - "description": "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes.", + "description": "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological outcomes.", "from_schema": "https://w3id.org/biolink/vocab/", "mixin": true, "slot_usage": {}, @@ -34054,6 +34722,47 @@ "comments": [ "This is roughly the model used by biolink and ontobio at the moment" ], + "examples": [ + { + "object": { + "subject": "NCBIGene:6910", + "predicate": "biolink:acts_upstream_of", + "object": "GO:1901846", + "category": "biolink:Association", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "PMID:15289437" + ] + }, + "@type": "Example" + }, + { + "object": { + "subject": "NCBIGene:4357", + "predicate": "biolink:enables", + "object": "GO:0005515", + "category": "biolink:Association", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "PMID:32296183" + ] + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:114566", + "predicate": "biolink:subclass_of", + "object": "CHEBI:38166", + "category": "biolink:Association", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "OBAN:association", @@ -35366,6 +36075,38 @@ "name": "ChemicalEntityToChemicalEntityAssociation", "definition_uri": "https://w3id.org/biolink/vocab/ChemicalEntityToChemicalEntityAssociation", "description": "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.", + "examples": [ + { + "object": { + "subject": "CHEBI:85990", + "predicate": "biolink:has_metabolite", + "object": "PUBCHEM.COMPOUND:155543741", + "category": "biolink:ChemicalEntityToChemicalEntityAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "PMID:22344701" + ], + "species_context_qualifier": "NCBITaxon:9606" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:85973", + "predicate": "biolink:has_metabolite", + "object": "UNII:9O1PTP64VA", + "category": "biolink:ChemicalEntityToChemicalEntityAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "PMID:22936313" + ], + "species_context_qualifier": "NCBITaxon:9606" + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "slots": [ @@ -35431,6 +36172,7 @@ { "name": "ReactionToParticipantAssociation", "definition_uri": "https://w3id.org/biolink/vocab/ReactionToParticipantAssociation", + "description": "An association between a biochemical reaction and a participating molecular entity, qualified by the stoichiometry, the side (reactant vs. product) on which the participant appears, and the direction of the reaction.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "ChemicalEntityToChemicalEntityAssociation", "slots": [ @@ -35500,6 +36242,7 @@ { "name": "ReactionToCatalystAssociation", "definition_uri": "https://w3id.org/biolink/vocab/ReactionToCatalystAssociation", + "description": "A specialization of reaction-to-participant association in which the participant is a gene or gene product (e.g., an enzyme) that catalyses the reaction.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "ReactionToParticipantAssociation", "slots": [ @@ -35633,6 +36376,74 @@ "name": "ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation", "definition_uri": "https://w3id.org/biolink/vocab/ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation", "description": "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.", + "examples": [ + { + "object": { + "subject": "CHEBI:167638", + "predicate": "biolink:contraindicated_in", + "object": "UMLS:C0271149", + "category": "biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:25879", + "predicate": "biolink:contraindicated_in", + "object": "UMLS:C0234976", + "category": "biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "PUBCHEM.COMPOUND:134612761", + "predicate": "biolink:diagnoses", + "object": "UMLS:C1720505", + "category": "biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:82720", + "predicate": "biolink:preventative_for_condition", + "object": "UMLS:C1320716", + "category": "biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:6919", + "predicate": "biolink:treats", + "object": "EFO:1001421", + "category": "biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:135361", + "predicate": "biolink:treats", + "object": "MONDO:0005324", + "category": "biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "narrow_mappings": [ "SIO:000993" @@ -36212,7 +37023,7 @@ { "name": "NamedThingAssociatedWithLikelihoodOfNamedThingAssociation", "definition_uri": "https://w3id.org/biolink/vocab/NamedThingAssociatedWithLikelihoodOfNamedThingAssociation", - "description": "", + "description": "An association in which the subject entity is linked to the likelihood of the object entity occurring, manifesting, or being observed. Subject and object may each be qualified by aspect and context, and the association may be further qualified by a population context.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "slots": [ @@ -36289,6 +37100,47 @@ "name": "ChemicalGeneInteractionAssociation", "definition_uri": "https://w3id.org/biolink/vocab/ChemicalGeneInteractionAssociation", "description": "describes an interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)", + "examples": [ + { + "object": { + "subject": "CHEBI:135370", + "predicate": "biolink:directly_physically_interacts_with", + "object": "UniProtKB:P0DP23", + "category": "biolink:ChemicalGeneInteractionAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:4779", + "predicate": "biolink:directly_physically_interacts_with", + "object": "NCBIGene:3269", + "category": "biolink:ChemicalGeneInteractionAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "http://www.accessdata.fda.gov/drugsatfda_docs/label/2003/20706slr011_emadine_lbl.pdf" + ] + }, + "@type": "Example" + }, + { + "object": { + "subject": "UNII:OP35X9610Y", + "predicate": "biolink:interacts_with", + "object": "NCBIGene:2690", + "category": "biolink:ChemicalGeneInteractionAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "https://www.accessdata.fda.gov/drugsatfda_docs/label/2021/761177Orig1s000lbl.pdf" + ] + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "broad_mappings": [ "SIO:001257" @@ -36371,6 +37223,30 @@ "notes": [ "Using macromolecular machine should cover cases of gene-protein conflation." ], + "examples": [ + { + "object": { + "subject": "NCBIGene:6530", + "predicate": "biolink:has_substrate", + "object": "CHEBI:5557", + "category": "biolink:MacromolecularMachineHasSubstrateAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "NCBIGene:50719", + "predicate": "biolink:has_substrate", + "object": "UNII:UID84303EL", + "category": "biolink:MacromolecularMachineHasSubstrateAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "slots": [ @@ -36640,6 +37516,89 @@ "name": "ChemicalAffectsGeneAssociation", "definition_uri": "https://w3id.org/biolink/vocab/ChemicalAffectsGeneAssociation", "description": "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)", + "examples": [ + { + "object": { + "subject": "PUBCHEM.COMPOUND:168290237", + "predicate": "biolink:affects", + "object": "NCBIGene:200424", + "category": "biolink:ChemicalAffectsGeneAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "automated_agent", + "publications": [ + "PMID:35978680" + ], + "object_aspect_qualifier": "activity", + "object_direction_qualifier": "decreased", + "causal_mechanism_qualifier": "inhibition", + "qualified_predicate": "biolink:causes", + "species_context_qualifier": "NCBITaxon:9606" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:91447", + "predicate": "biolink:directly_physically_interacts_with", + "object": "NCBIGene:3313", + "category": "biolink:ChemicalAffectsGeneAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "automated_agent", + "publications": [ + "PMID:29928781" + ], + "causal_mechanism_qualifier": "binding", + "species_context_qualifier": "NCBITaxon:9606" + }, + "@type": "Example" + }, + { + "object": { + "subject": "UNII:5V9KLZ54CY", + "predicate": "biolink:has_substrate", + "object": "NCBIGene:5244", + "category": "biolink:ChemicalAffectsGeneAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "PMID:20190787" + ], + "species_context_qualifier": "NCBITaxon:9606" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEMBL.COMPOUND:CHEMBL1743027", + "predicate": "biolink:interacts_with", + "object": "NCBIGene:768", + "category": "biolink:ChemicalAffectsGeneAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "http://www.wilex.de/portfolio-english/rencarex/therapeutic-target/", + "PMID:11941456" + ], + "species_context_qualifier": "NCBITaxon:9606" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:3546", + "predicate": "biolink:affects", + "object": "NCBIGene:4790", + "category": "biolink:ChemicalAffectsGeneAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "object_aspect_qualifier": "activity", + "object_direction_qualifier": "decreased", + "causal_mechanism_qualifier": "inhibition", + "qualified_predicate": "biolink:causes" + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "ChemicalAffectsBiologicalEntityAssociation", "slots": [ @@ -36721,7 +37680,39 @@ "description": "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)", "examples": [ { - "value": "JsonObj(subject='TRPC4', predicate='affects', qualified_predicate='causes', object='Barium', object_aspect_qualifier='transport', object_direction_qualifier='increased')", + "object": { + "subject": "NCBIGene:6616", + "predicate": "biolink:affects", + "object": "CHEMBL.COMPOUND:CHEMBL3707322", + "category": "biolink:GeneAffectsChemicalAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "CHEMBL.DOCUMENT:CHEMBL2107839", + "https://www.accessdata.fda.gov/drugsatfda_docs/label/2024/761225s000lbl.pdf" + ], + "subject_aspect_qualifier": "hydrolysis", + "subject_direction_qualifier": "increased", + "qualified_predicate": "biolink:causes", + "species_context_qualifier": "NCBITaxon:9606" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:3172", + "predicate": "biolink:has_substrate", + "object": "NCBIGene:6530", + "category": "biolink:GeneAffectsChemicalAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "ISBN:9780702034718 PP. 190-191", + "PMID:18071295", + "PMID:9142404" + ], + "species_context_qualifier": "NCBITaxon:9606" + }, "@type": "Example" } ], @@ -37028,6 +38019,7 @@ { "name": "DiseaseToEntityAssociationMixin", "definition_uri": "https://w3id.org/biolink/vocab/DiseaseToEntityAssociationMixin", + "description": "A mixin applied to any association whose subject (source node) is a disease.", "from_schema": "https://w3id.org/biolink/vocab/", "mixin": true, "slots": [ @@ -37325,6 +38317,7 @@ { "name": "EntityToPhenotypicFeatureAssociationMixin", "definition_uri": "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin", + "description": "A mixin applied to any association whose object (target node) is a phenotypic feature.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "EntityToFeatureOrDiseaseQualifiersMixin", "mixin": true, @@ -37360,6 +38353,7 @@ { "name": "PhenotypicFeatureToEntityAssociationMixin", "definition_uri": "https://w3id.org/biolink/vocab/PhenotypicFeatureToEntityAssociationMixin", + "description": "A mixin applied to any association whose subject (source node) is a phenotypic feature.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "FeatureOrDiseaseQualifiersToEntityMixin", "mixin": true, @@ -38398,6 +39392,7 @@ { "name": "GeneToPhenotypicFeatureAssociation", "definition_uri": "https://w3id.org/biolink/vocab/GeneToPhenotypicFeatureAssociation", + "description": "An association between a gene or gene product and a phenotypic feature, where variation in the gene is correlated with the phenotypic feature.", "comments": [ "NCIT:R176 refers to the inverse relationship", "for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype", @@ -38492,11 +39487,36 @@ { "name": "GeneToDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation", + "description": "An association between a gene or gene product and a disease, where variation in the gene is correlated with the disease.", "comments": [ "NCIT:R176 refers to the inverse relationship", "for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a disease", "if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children." ], + "examples": [ + { + "object": { + "subject": "NCBIGene:60", + "predicate": "biolink:associated_with", + "object": "MONDO:0017579", + "category": "biolink:GeneToDiseaseAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "UniProtKB:P11274-1", + "predicate": "biolink:associated_with", + "object": "MONDO:0011996", + "category": "biolink:GeneToDiseaseAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "exact_mappings": [ "SIO:000983" @@ -38577,6 +39597,7 @@ { "name": "CausalGeneToDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation", + "description": "An association between a gene and a disease where variation in the gene has been shown to have a causal role in the disease.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "mixins": [ @@ -38649,6 +39670,31 @@ { "name": "CorrelatedGeneToDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation", + "description": "An association between a gene (or gene product) and a disease for which the gene is statistically correlated with the disease rather than asserted as causal. Such associations typically derive from GWAS, co-occurrence analyses, or other statistical methods, and are annotated with scores such as a z-score or a diseases confidence score.", + "examples": [ + { + "object": { + "subject": "NCBIGene:8506", + "predicate": "biolink:occurs_together_in_literature_with", + "object": "MONDO:0004585", + "category": "biolink:CorrelatedGeneToDiseaseAssociation", + "knowledge_level": "text_co_occurrence", + "agent_type": "data_analysis_pipeline" + }, + "@type": "Example" + }, + { + "object": { + "subject": "UniProtKB:Q2KHT3-1", + "predicate": "biolink:occurs_together_in_literature_with", + "object": "MONDO:0005578", + "category": "biolink:CorrelatedGeneToDiseaseAssociation", + "knowledge_level": "text_co_occurrence", + "agent_type": "data_analysis_pipeline" + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "mixins": [ @@ -38729,6 +39775,7 @@ { "name": "DruggableGeneToDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/DruggableGeneToDiseaseAssociation", + "description": "An association between a gene (or gene product) and a disease in which the gene is classified by its druggability (e.g., via the IDG/Pharos target development-level tiers).", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "GeneToDiseaseAssociation", "mixins": [ @@ -38810,6 +39857,7 @@ { "name": "PhenotypicFeatureToDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/PhenotypicFeatureToDiseaseAssociation", + "description": "An association between a phenotypic feature (sign or symptom) and a disease, where the phenotypic feature is a manifestation or clinical indicator of the disease.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "mixins": [ @@ -39173,6 +40221,7 @@ { "name": "VariantToPhenotypicFeatureAssociation", "definition_uri": "https://w3id.org/biolink/vocab/VariantToPhenotypicFeatureAssociation", + "description": "An association between a sequence variant and a phenotypic feature, in which the allele state of the variant is linked to the manifestation of the phenotype.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "mixins": [ @@ -39253,6 +40302,7 @@ { "name": "VariantToDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/VariantToDiseaseAssociation", + "description": "An association between a sequence variant and a disease, in which the allele state of the variant is linked to the disease state.", "comments": [ "TODO decide no how to model pathogenicity" ], @@ -39331,6 +40381,7 @@ { "name": "GenotypeToDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/GenotypeToDiseaseAssociation", + "description": "An association between a genotype and a disease, in which the genotype (typically a combination of alleles at one or more loci) is linked to the disease state.", "comments": [ "TODO decide no how to model pathogenicity" ], @@ -39424,6 +40475,7 @@ { "name": "GeneAsAModelOfDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/GeneAsAModelOfDiseaseAssociation", + "description": "An association in which a gene (e.g., a model-organism ortholog of a known disease gene) serves as a model of a human disease - for example, because mutants of the gene recapitulate core features of the disease.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "GeneToDiseaseAssociation", "mixins": [ @@ -39504,6 +40556,7 @@ { "name": "VariantAsAModelOfDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/VariantAsAModelOfDiseaseAssociation", + "description": "An association in which a sequence variant serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "VariantToDiseaseAssociation", "mixins": [ @@ -39580,6 +40633,7 @@ { "name": "GenotypeAsAModelOfDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/GenotypeAsAModelOfDiseaseAssociation", + "description": "An association in which a genotype serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "GenotypeToDiseaseAssociation", "mixins": [ @@ -39656,6 +40710,7 @@ { "name": "CellLineAsAModelOfDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/CellLineAsAModelOfDiseaseAssociation", + "description": "An association in which a cell line - typically derived from an organismal entity with a disease state - serves as a model for that disease in experimental settings.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "CellLineToDiseaseOrPhenotypicFeatureAssociation", "mixins": [ @@ -39735,6 +40790,7 @@ { "name": "OrganismalEntityAsAModelOfDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/OrganismalEntityAsAModelOfDiseaseAssociation", + "description": "An association in which an organismal entity (e.g., a strain or breed) serves as a model of a disease, either because it has a natural predisposition to the disease or was bred or engineered specifically to recapitulate it.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "mixins": [ @@ -39811,6 +40867,7 @@ { "name": "OrganismToOrganismAssociation", "definition_uri": "https://w3id.org/biolink/vocab/OrganismToOrganismAssociation", + "description": "An association between two individual organisms (e.g., symbiosis, parasitism, predation, or other inter-organism relationships).", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "slots": [ @@ -39876,6 +40933,7 @@ { "name": "TaxonToTaxonAssociation", "definition_uri": "https://w3id.org/biolink/vocab/TaxonToTaxonAssociation", + "description": "An association between two organism taxa, capturing ecological or evolutionary relationships between the taxa (e.g., a host-pathogen relationship or shared habitat).", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "slots": [ @@ -39941,6 +40999,7 @@ { "name": "GeneHasVariantThatContributesToDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/GeneHasVariantThatContributesToDiseaseAssociation", + "description": "A gene-to-disease association that is asserted on the grounds that the gene harbours a sequence variant that contributes to the disease. Qualifies the gene with the form or variant that underlies the contribution.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "GeneToDiseaseAssociation", "slots": [ @@ -40551,6 +41610,114 @@ { "name": "GeneToGoTermAssociation", "definition_uri": "https://w3id.org/biolink/vocab/GeneToGoTermAssociation", + "description": "A functional association between a gene (or gene product or macromolecular complex) and a Gene Ontology (GO) term describing the molecular function, biological process, or cellular component in which it participates.", + "examples": [ + { + "object": { + "subject": "NCBIGene:25595", + "predicate": "biolink:active_in", + "object": "GO:0015630", + "category": "biolink:GeneToGoTermAssociation", + "knowledge_level": "prediction", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "NCBIGene:20502", + "predicate": "biolink:acts_upstream_of", + "object": "GO:0042403", + "category": "biolink:GeneToGoTermAssociation", + "knowledge_level": "prediction", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "NCBIGene:308911", + "predicate": "biolink:acts_upstream_of_negative_effect", + "object": "GO:1903450", + "category": "biolink:GeneToGoTermAssociation", + "knowledge_level": "prediction", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "NCBIGene:101148", + "predicate": "biolink:acts_upstream_of_or_within", + "object": "GO:0031669", + "category": "biolink:GeneToGoTermAssociation", + "knowledge_level": "prediction", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "NCBIGene:18072", + "predicate": "biolink:acts_upstream_of_or_within_positive_effect", + "object": "GO:0006915", + "category": "biolink:GeneToGoTermAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent", + "publications": [ + "PMID:17573818" + ] + }, + "@type": "Example" + }, + { + "object": { + "subject": "NCBIGene:12168", + "predicate": "biolink:colocalizes_with", + "object": "GO:0005901", + "category": "biolink:GeneToGoTermAssociation", + "knowledge_level": "prediction", + "agent_type": "automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "NCBIGene:303888", + "predicate": "biolink:contributes_to", + "object": "GO:0160270", + "category": "biolink:GeneToGoTermAssociation", + "knowledge_level": "prediction", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "NCBIGene:12193", + "predicate": "biolink:enables", + "object": "GO:0046872", + "category": "biolink:GeneToGoTermAssociation", + "knowledge_level": "prediction", + "agent_type": "automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "NCBIGene:258177", + "predicate": "biolink:located_in", + "object": "GO:0016020", + "category": "biolink:GeneToGoTermAssociation", + "knowledge_level": "prediction", + "agent_type": "automated_agent", + "publications": [ + "PMID:14611657" + ] + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "aliases": [ "functional association" @@ -40621,6 +41788,56 @@ { "name": "EntityToDiseaseAssociation", "definition_uri": "https://w3id.org/biolink/vocab/EntityToDiseaseAssociation", + "description": "An association between any entity and a disease, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases.", + "examples": [ + { + "object": { + "subject": "CHEBI:50681", + "predicate": "biolink:in_clinical_trials_for", + "object": "MONDO:0971091", + "category": "biolink:EntityToDiseaseAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:9150", + "predicate": "biolink:treats", + "object": "UMLS:C0520863", + "category": "biolink:EntityToDiseaseAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:28077", + "predicate": "biolink:applied_to_treat", + "object": "MONDO:0005011", + "category": "biolink:EntityToDiseaseAssociation", + "knowledge_level": "observation", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "RXCUI:1367436", + "predicate": "biolink:contraindicated_in", + "object": "MONDO:0004981", + "category": "biolink:EntityToDiseaseAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_validation_of_automated_agent", + "publications": [ + "a280f164-2833-4f37-96e3-a857c91f77f2" + ] + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "slots": [ @@ -40689,6 +41906,60 @@ { "name": "EntityToPhenotypicFeatureAssociation", "definition_uri": "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociation", + "description": "An association between any entity and a phenotypic feature, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases.", + "examples": [ + { + "object": { + "subject": "GTOPDB:13663", + "predicate": "biolink:in_clinical_trials_for", + "object": "NCIT:C146753", + "category": "biolink:EntityToPhenotypicFeatureAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:6339", + "predicate": "biolink:treats", + "object": "HP:0001822", + "category": "biolink:EntityToPhenotypicFeatureAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "CHEBI:78538", + "predicate": "biolink:applied_to_treat", + "object": "MONDO:0005294", + "category": "biolink:EntityToPhenotypicFeatureAssociation", + "knowledge_level": "observation", + "agent_type": "manual_validation_of_automated_agent" + }, + "@type": "Example" + }, + { + "object": { + "subject": "RXCUI:617430", + "predicate": "biolink:contraindicated_in", + "object": "HP:0001410", + "category": "biolink:EntityToPhenotypicFeatureAssociation", + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_validation_of_automated_agent", + "publications": [ + "2970fe7e-9e1f-47aa-85ad-663ee15c7e06", + "a5fa252a-d39e-4099-a230-b665fbb97a80", + "b897c800-24a2-4e76-8668-498c5515c3d0", + "babf3b8d-f2ce-407d-9407-728c45eb19ee", + "d74e93e5-11c9-434e-a60c-4a4f911dd0f8" + ] + }, + "@type": "Example" + } + ], "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "slots": [ @@ -41215,6 +42486,7 @@ { "name": "AnatomicalEntityToAnatomicalEntityAssociation", "definition_uri": "https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityAssociation", + "description": "An abstract parent class for associations between two anatomical entities, such as part-of, develops-from, or other mereological and ontogenic relationships.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "abstract": true, @@ -41818,6 +43090,7 @@ { "name": "OrganismTaxonToEnvironmentAssociation", "definition_uri": "https://w3id.org/biolink/vocab/OrganismTaxonToEnvironmentAssociation", + "description": "An abstract association between an organism taxon and an environmental context (e.g., a habitat, biome, or ecological setting) in which the taxon occurs.", "from_schema": "https://w3id.org/biolink/vocab/", "is_a": "Association", "abstract": true, @@ -41882,9 +43155,9 @@ ], "metamodel_version": "1.7.0", "source_file": "biolink_model.yaml", - "source_file_date": "2026-04-21T19:05:19", - "source_file_size": 464036, - "generation_date": "2026-04-21T19:05:25", + "source_file_date": "2026-04-21T12:14:59", + "source_file_size": 509081, + "generation_date": "2026-04-21T12:15:16", "@type": "SchemaDefinition", "@context": [ "project/jsonld/biolink_model.context.jsonld", diff --git a/project/jsonschema/biolink_model.schema.json b/project/jsonschema/biolink_model.schema.json index 1a6ac15e8..ba0febf31 100644 --- a/project/jsonschema/biolink_model.schema.json +++ b/project/jsonschema/biolink_model.schema.json @@ -132,6 +132,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -266,6 +267,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -415,6 +417,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -581,6 +584,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -608,7 +612,7 @@ "type": "object" }, "AgentTypeEnum": { - "description": "", + "description": "An enumeration of agent types responsible for generating a statement of knowledge, as defined by the Translator Knowledge Level / Agent Type (KL/AT) standard. Values distinguish human (manual) agents from automated agents (including data analysis pipelines, computational models, text-mining agents, image-processing agents) and mixed cases such as manual validation of automated output.", "enum": [ "manual_agent", "automated_agent", @@ -624,7 +628,7 @@ }, "AnatomicalEntity": { "additionalProperties": false, - "description": "A subcellular location, cell type or gross anatomical part", + "description": "A part of a cellular organism at or above the granularity of a protein complex. This is a grouping class with three concrete subclasses that should be preferred when applicable: \"biolink:Cell\" for whole cells, \"biolink:CellularComponent\" for subcellular and intracellular structures (organelles, membranes, bacterial flagella, etc.), and \"biolink:GrossAnatomcialStructure\" for multicellular parts (tissues, organs, body parts). Excludes viral and other acellular biological entities.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -747,6 +751,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -1025,6 +1030,15 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:has_active_ingredient", + "biolink:has_excipient", + "biolink:has_food_component", + "biolink:has_nutrient", + "biolink:has_part", + "biolink:has_plasma_membrane_part", + "biolink:has_variant_part" + ], "type": "string" }, "primary_knowledge_source": { @@ -1443,6 +1457,15 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:food_component_of", + "biolink:is_active_ingredient_of", + "biolink:is_excipient_of", + "biolink:nutrient_of", + "biolink:part_of", + "biolink:plasma_membrane_part_of", + "biolink:variant_part_of" + ], "type": "string" }, "primary_knowledge_source": { @@ -1861,6 +1884,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:develops_from" + ], "type": "string" }, "primary_knowledge_source": { @@ -2028,7 +2054,7 @@ "type": "object" }, "ApprovalStatusEnum": { - "description": "", + "description": "An enumeration of regulatory and development milestones for a drug or therapeutic, spanning discovery, preclinical research, FDA clinical trial phases (1-4), special review designations (e.g., fast track, breakthrough therapy, priority review), regular FDA approval, and post-approval withdrawal.", "enum": [ "discovery_and_development_phase", "preclinical_research_phase", @@ -2106,6 +2132,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -2171,6 +2198,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -2225,6 +2253,7 @@ "type": "string" }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -2255,6 +2284,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -2837,6 +2867,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -2989,6 +3020,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -3017,7 +3049,7 @@ }, "Behavior": { "additionalProperties": false, - "description": "", + "description": "The internally coordinated responses (actions or inactions) of organisms (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3170,6 +3202,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -3409,11 +3442,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -3582,11 +3612,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -3864,6 +3891,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -4022,6 +4050,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -4219,6 +4248,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -4400,6 +4430,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -5096,6 +5127,9 @@ }, "predicate": { "description": "One biological processes or activities is a subclass of another.", + "enum": [ + "biolink:subclass_of" + ], "type": "string" }, "primary_knowledge_source": { @@ -5514,6 +5548,17 @@ }, "predicate": { "description": "Relationship in which a biological process has the participation of a gene or gene product or gene family in a (e.g., pathway has participant gene product).", + "enum": [ + "biolink:actively_involves", + "biolink:can_be_carried_out_by", + "biolink:consumes", + "biolink:enabled_by", + "biolink:has_catalyst", + "biolink:has_input", + "biolink:has_output", + "biolink:has_participant", + "biolink:has_substrate" + ], "type": "string" }, "primary_knowledge_source": { @@ -5682,7 +5727,7 @@ }, "BiologicalSex": { "additionalProperties": false, - "description": "", + "description": "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5809,6 +5854,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -6009,6 +6055,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -6092,6 +6139,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -6143,6 +6191,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -6193,6 +6242,7 @@ "type": "array" }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -6253,7 +6303,7 @@ }, "BookChapter": { "additionalProperties": false, - "description": "", + "description": "A section of a book that forms a discrete unit of a larger published work and may be independently authored or cited.", "properties": { "authors": { "description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", @@ -6315,6 +6365,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -6366,6 +6417,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -6420,6 +6472,7 @@ "type": "string" }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -6450,6 +6503,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -6541,7 +6595,7 @@ ] }, "has_biological_sex": { - "description": "The biological sex of the entity (e.g., male or female) regarding a case description from a phenopacket", + "description": "The biological sex of the entity regarding a case description from a phenopacket", "type": [ "string", "null" @@ -6617,6 +6671,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -7699,11 +7754,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -7879,11 +7931,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -8120,6 +8169,7 @@ ] }, "has_zygosity": { + "description": "The zygosity characterising a genotype or nucleic acid entity at a particular locus.", "type": [ "string", "null" @@ -8414,7 +8464,7 @@ }, "CausalGeneToDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a gene and a disease where variation in the gene has been shown to have a causal role in the disease.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -8751,11 +8801,8 @@ "description": "gene in which variation is shown to cause the disease." }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -8864,7 +8911,7 @@ "type": "object" }, "CausalMechanismQualifierEnum": { - "description": "", + "description": "An enumeration used as a qualifier to specify the causal or pharmacologic mechanism by which an effect is exerted in an association (e.g., agonism, antagonism, inverse agonism, allosteric modulation, activation, inhibition, and their competitive or partial variants).", "enum": [ "modulation", "allosteric_modulation", @@ -8972,7 +9019,7 @@ }, "Cell": { "additionalProperties": false, - "description": "", + "description": "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -9095,6 +9142,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -9123,7 +9171,7 @@ }, "CellLine": { "additionalProperties": false, - "description": "", + "description": "A cultured cell population that is genetically stable and homogeneous, sharing a common propagation history through successive passages in culture.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -9246,6 +9294,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -9274,7 +9323,7 @@ }, "CellLineAsAModelOfDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association in which a cell line - typically derived from an organismal entity with a disease state - serves as a model for that disease in experimental settings.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -9468,11 +9517,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -9566,6 +9612,9 @@ }, "predicate": { "description": "The relationship to the disease", + "enum": [ + "biolink:model_of" + ], "type": "string" }, "primary_knowledge_source": { @@ -9641,11 +9690,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -10331,6 +10377,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -10359,7 +10406,7 @@ }, "CellularOrganism": { "additionalProperties": false, - "description": "", + "description": "An organism that contains one or more cells belonging to the cellular lineages of life (Archaea, Bacteria, or Eukaryota), whose body consists of one or more cells. Distinguished from acellular biological entities such as viruses and viroids.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10482,6 +10529,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -10558,7 +10606,7 @@ }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", - "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" + "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", @@ -10725,6 +10773,7 @@ ] }, "object_context_qualifier": { + "description": "A qualifier describing the context in which the object of an association holds.", "type": [ "string", "null" @@ -10764,7 +10813,7 @@ }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement)." }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", @@ -10796,6 +10845,15 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:affects", + "biolink:ameliorates_condition", + "biolink:disrupts", + "biolink:exacerbates_condition", + "biolink:has_adverse_event", + "biolink:has_side_effect", + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -10817,6 +10875,9 @@ }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", + "enum": [ + "biolink:causes" + ], "type": [ "string", "null" @@ -10909,6 +10970,7 @@ ] }, "subject_context_qualifier": { + "description": "A qualifier describing the context in which the subject of an association holds.", "type": [ "string", "null" @@ -10952,7 +11014,7 @@ }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement)." }, "supporting_text": { "description": "The segment of text from a document that supports the mined assertion.", @@ -11052,7 +11114,7 @@ }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", - "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" + "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", @@ -11233,6 +11295,7 @@ ] }, "object_context_qualifier": { + "description": "A qualifier describing the context in which the object of an association holds.", "type": [ "string", "null" @@ -11272,7 +11335,7 @@ }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement)." }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", @@ -11304,6 +11367,15 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:affects", + "biolink:ameliorates_condition", + "biolink:disrupts", + "biolink:exacerbates_condition", + "biolink:has_adverse_event", + "biolink:has_side_effect", + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -11325,6 +11397,9 @@ }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", + "enum": [ + "biolink:causes" + ], "type": [ "string", "null" @@ -11417,6 +11492,7 @@ ] }, "subject_context_qualifier": { + "description": "A qualifier describing the context in which the subject of an association holds.", "type": [ "string", "null" @@ -11460,7 +11536,7 @@ }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement)." }, "supporting_documents": { "description": "One or more referenceable documents that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", @@ -11525,7 +11601,7 @@ "description": "A chemical entity is a physical entity that pertains to chemistry or biochemistry.", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -11656,7 +11732,7 @@ ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -11714,13 +11790,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -11999,6 +12076,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:was_tested_for_effect_on" + ], "type": "string" }, "primary_knowledge_source": { @@ -12166,7 +12246,7 @@ "type": "object" }, "ChemicalEntityDerivativeEnum": { - "description": "", + "description": "An enumeration of relationships by which one chemical entity is derived from another, e.g., a metabolite produced from a parent compound.", "enum": [ "metabolite" ], @@ -12429,6 +12509,9 @@ }, "predicate": { "description": "the direction is always from regulator to regulated", + "enum": [ + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -12861,6 +12944,238 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:active_in", + "biolink:actively_involved_in", + "biolink:actively_involves", + "biolink:acts_upstream_of", + "biolink:acts_upstream_of_negative_effect", + "biolink:acts_upstream_of_or_within", + "biolink:acts_upstream_of_or_within_negative_effect", + "biolink:acts_upstream_of_or_within_positive_effect", + "biolink:acts_upstream_of_positive_effect", + "biolink:adverse_event_of", + "biolink:affected_by", + "biolink:affects", + "biolink:affects_likelihood_of", + "biolink:affects_sensitivity_to", + "biolink:ameliorates_condition", + "biolink:amount_or_activity_decreased_by", + "biolink:amount_or_activity_increased_by", + "biolink:applied_to_treat", + "biolink:associated_with", + "biolink:associated_with_decreased_likelihood_of", + "biolink:associated_with_increased_likelihood_of", + "biolink:associated_with_likelihood_of", + "biolink:associated_with_resistance_to", + "biolink:associated_with_response_to", + "biolink:associated_with_sensitivity_to", + "biolink:author", + "biolink:beneficial_in_models_for", + "biolink:binds", + "biolink:biomarker_for", + "biolink:can_be_carried_out_by", + "biolink:capable_of", + "biolink:catalyzes", + "biolink:caused_by", + "biolink:causes", + "biolink:chemically_similar_to", + "biolink:coexists_with", + "biolink:coexpressed_with", + "biolink:colocalizes_with", + "biolink:completed_by", + "biolink:condition_ameliorated_by", + "biolink:condition_associated_with_gene", + "biolink:condition_exacerbated_by", + "biolink:condition_predisposed_by", + "biolink:condition_prevented_by", + "biolink:condition_promoted_by", + "biolink:consumed_by", + "biolink:consumes", + "biolink:contains_process", + "biolink:contraindicated_in", + "biolink:contributes_to", + "biolink:contribution_from", + "biolink:contributor", + "biolink:correlated_with", + "biolink:decreased_amount_in", + "biolink:decreased_likelihood_associated_with", + "biolink:decreases_amount_or_activity_of", + "biolink:decreases_sensitivity_to", + "biolink:derives_from", + "biolink:derives_into", + "biolink:develops_from", + "biolink:develops_into", + "biolink:diagnoses", + "biolink:directly_physically_interacts_with", + "biolink:disease_has_basis_in", + "biolink:disrupted_by", + "biolink:disrupts", + "biolink:editor", + "biolink:enabled_by", + "biolink:enables", + "biolink:exacerbates_condition", + "biolink:expressed_in", + "biolink:expresses", + "biolink:food_component_of", + "biolink:gene_associated_with_condition", + "biolink:gene_fusion_with", + "biolink:gene_product_of", + "biolink:genetic_association", + "biolink:genetic_neighborhood_of", + "biolink:genetically_associated_with", + "biolink:genetically_interacts_with", + "biolink:has_active_component", + "biolink:has_active_ingredient", + "biolink:has_adverse_event", + "biolink:has_author", + "biolink:has_biomarker", + "biolink:has_catalyst", + "biolink:has_completed", + "biolink:has_contraindication", + "biolink:has_contributor", + "biolink:has_decreased_amount", + "biolink:has_editor", + "biolink:has_excipient", + "biolink:has_food_component", + "biolink:has_frameshift_variant", + "biolink:has_gene_product", + "biolink:has_increased_amount", + "biolink:has_input", + "biolink:has_manifestation", + "biolink:has_metabolite", + "biolink:has_missense_variant", + "biolink:has_mode_of_inheritance", + "biolink:has_molecular_consequence", + "biolink:has_nearby_variant", + "biolink:has_negative_upstream_actor", + "biolink:has_negative_upstream_or_within_actor", + "biolink:has_non_coding_variant", + "biolink:has_nonsense_variant", + "biolink:has_not_completed", + "biolink:has_nutrient", + "biolink:has_output", + "biolink:has_part", + "biolink:has_participant", + "biolink:has_phenotype", + "biolink:has_plasma_membrane_part", + "biolink:has_positive_upstream_actor", + "biolink:has_positive_upstream_or_within_actor", + "biolink:has_provider", + "biolink:has_publisher", + "biolink:has_sequence_location", + "biolink:has_sequence_variant", + "biolink:has_side_effect", + "biolink:has_splice_site_variant", + "biolink:has_substrate", + "biolink:has_synonymous_variant", + "biolink:has_target", + "biolink:has_upstream_actor", + "biolink:has_upstream_or_within_actor", + "biolink:has_variant_part", + "biolink:homologous_to", + "biolink:in_cell_population_with", + "biolink:in_clinical_trials_for", + "biolink:in_complex_with", + "biolink:in_linkage_disequilibrium_with", + "biolink:in_pathway_with", + "biolink:in_preclinical_trials_for", + "biolink:in_taxon", + "biolink:increased_amount_of", + "biolink:increased_likelihood_associated_with", + "biolink:increases_amount_or_activity_of", + "biolink:increases_sensitivity_to", + "biolink:indirectly_physically_interacts_with", + "biolink:interacts_with", + "biolink:is_active_ingredient_of", + "biolink:is_diagnosed_by", + "biolink:is_excipient_of", + "biolink:is_frameshift_variant_of", + "biolink:is_input_of", + "biolink:is_metabolite_of", + "biolink:is_missense_variant_of", + "biolink:is_molecular_consequence_of", + "biolink:is_nearby_variant_of", + "biolink:is_non_coding_variant_of", + "biolink:is_nonsense_variant_of", + "biolink:is_output_of", + "biolink:is_sequence_variant_of", + "biolink:is_side_effect_of", + "biolink:is_splice_site_variant_of", + "biolink:is_substrate_of", + "biolink:is_synonymous_variant_of", + "biolink:lacks_part", + "biolink:likelihood_affected_by", + "biolink:likelihood_associated_with", + "biolink:located_in", + "biolink:location_of", + "biolink:manifestation_of", + "biolink:mentioned_by", + "biolink:mentions", + "biolink:missing_from", + "biolink:mode_of_inheritance_of", + "biolink:model_of", + "biolink:models", + "biolink:models_demonstrating_benefits_for", + "biolink:negatively_correlated_with", + "biolink:not_completed_by", + "biolink:nutrient_of", + "biolink:occurs_in", + "biolink:occurs_in_disease", + "biolink:occurs_together_in_literature_with", + "biolink:opposite_of", + "biolink:orthologous_to", + "biolink:overlaps", + "biolink:paralogous_to", + "biolink:part_of", + "biolink:participates_in", + "biolink:pharmacologically_interacts_with", + "biolink:phenotype_of", + "biolink:physically_interacts_with", + "biolink:plasma_membrane_part_of", + "biolink:positively_correlated_with", + "biolink:preceded_by", + "biolink:precedes", + "biolink:predisposes_to_condition", + "biolink:preventative_for_condition", + "biolink:produced_by", + "biolink:produces", + "biolink:promotes_condition", + "biolink:provider", + "biolink:publisher", + "biolink:regulated_by", + "biolink:regulates", + "biolink:related_condition", + "biolink:related_to_at_instance_level", + "biolink:resistance_associated_with", + "biolink:response_associated_with", + "biolink:sensitivity_affected_by", + "biolink:sensitivity_associated_with", + "biolink:sensitivity_decreased_by", + "biolink:sensitivity_increased_by", + "biolink:sequence_location_of", + "biolink:similar_to", + "biolink:studied_to_treat", + "biolink:subject_of_treatment_application_or_study_for_treatment_by", + "biolink:target_for", + "biolink:taxon_of", + "biolink:temporally_related_to", + "biolink:tested_by_clinical_trials_of", + "biolink:tested_by_preclinical_trials_of", + "biolink:transcribed_from", + "biolink:transcribed_to", + "biolink:translates_to", + "biolink:translation_of", + "biolink:treated_by", + "biolink:treated_in_studies_by", + "biolink:treatment_applications_from", + "biolink:treats", + "biolink:treats_or_applied_or_studied_to_treat", + "biolink:variant_part_of", + "biolink:was_tested_for_effect_of", + "biolink:was_tested_for_effect_on", + "biolink:xenologous_to" + ], "type": "string" }, "primary_knowledge_source": { @@ -13303,6 +13618,10 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:derives_into", + "biolink:has_metabolite" + ], "type": "string" }, "primary_knowledge_source": { @@ -14959,6 +15278,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -15035,7 +15355,7 @@ }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", - "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" + "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", @@ -15226,6 +15546,7 @@ ] }, "object_context_qualifier": { + "description": "A qualifier describing the context in which the object of an association holds.", "type": [ "string", "null" @@ -15265,7 +15586,7 @@ }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement)." }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", @@ -15297,6 +15618,18 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:binds", + "biolink:directly_physically_interacts_with", + "biolink:gene_fusion_with", + "biolink:genetic_neighborhood_of", + "biolink:genetically_interacts_with", + "biolink:indirectly_physically_interacts_with", + "biolink:interacts_with", + "biolink:pharmacologically_interacts_with", + "biolink:physically_interacts_with", + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -15399,6 +15732,7 @@ ] }, "subject_context_qualifier": { + "description": "A qualifier describing the context in which the subject of an association holds.", "type": [ "string", "null" @@ -15438,7 +15772,7 @@ }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement)." }, "supporting_text": { "description": "The segment of text from a document that supports the mined assertion.", @@ -15493,7 +15827,7 @@ "description": "A chemical mixture is a chemical entity composed of two or more molecular entities.", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -15632,14 +15966,14 @@ ] }, "is_supplement": { - "description": "", + "description": "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food.", "type": [ "string", "null" ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -15697,13 +16031,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -15736,7 +16071,7 @@ "properties": { "FDA_adverse_event_level": { "$ref": "#/$defs/FDAIDAAdverseEventEnum", - "description": "" + "description": "The level or severity grade of an adverse event as classified by FDA adverse-event terminology, drawn from FDAIDAAdverseEventEnum; used on adverse-event associations." }, "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -15930,11 +16265,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -16028,6 +16360,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:has_adverse_event" + ], "type": "string" }, "primary_knowledge_source": { @@ -16103,11 +16438,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -16415,11 +16747,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -16513,6 +16842,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:has_side_effect" + ], "type": "string" }, "primary_knowledge_source": { @@ -16588,11 +16920,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -16900,11 +17229,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -16998,6 +17324,17 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:ameliorates_condition", + "biolink:applied_to_treat", + "biolink:beneficial_in_models_for", + "biolink:in_clinical_trials_for", + "biolink:in_preclinical_trials_for", + "biolink:preventative_for_condition", + "biolink:studied_to_treat", + "biolink:treats", + "biolink:treats_or_applied_or_studied_to_treat" + ], "type": "string" }, "primary_knowledge_source": { @@ -17073,11 +17410,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -17190,7 +17524,7 @@ "type": "object" }, "ChemicalOrGeneOrGeneProductFormOrVariantEnum": { - "description": "", + "description": "An enumeration used as a qualifier to indicate a specific form or variant of a chemical, gene, or gene product involved in an association (e.g., modified form, loss-of-function variant, gain-of-function variant, dominant-negative variant, polymorphic form, SNP form, mutant form, or analog form).", "enum": [ "genetic_variant_form", "modified_form", @@ -17335,6 +17669,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -17470,6 +17805,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -17497,7 +17833,7 @@ "type": "object" }, "ClinicalApprovalStatusEnum": { - "description": "", + "description": "An enumeration describing whether a chemical or therapy is approved for use in treating a specific condition (e.g., FDA-approved for a condition, not approved, off-label use, or withdrawn following approval).", "enum": [ "approved_for_condition", "fda_approved_for_condition", @@ -17638,6 +17974,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -17794,6 +18131,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -17929,6 +18267,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -18087,6 +18426,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -18115,7 +18455,7 @@ }, "ClinicalIntervention": { "additionalProperties": false, - "description": "", + "description": "A medical procedure, treatment, or action taken by healthcare professionals to modify the course of a disease or condition.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18221,6 +18561,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -18376,6 +18717,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -18532,6 +18874,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -18801,6 +19144,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -19099,6 +19443,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -19126,7 +19471,7 @@ }, "CodingSequence": { "additionalProperties": false, - "description": "", + "description": "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19256,6 +19601,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -19407,6 +19753,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -19480,6 +19827,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -19521,6 +19869,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -19544,6 +19893,7 @@ ] }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -19567,6 +19917,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -19595,7 +19946,7 @@ }, "ComplexChemicalExposure": { "additionalProperties": false, - "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.", + "description": "A complex chemical exposure is an intake of a chemical mixture, other than a drug.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19766,6 +20117,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -19797,7 +20149,7 @@ "description": "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -19936,14 +20288,14 @@ ] }, "is_supplement": { - "description": "", + "description": "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food.", "type": [ "string", "null" ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -20001,13 +20353,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -20142,6 +20495,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -20215,6 +20569,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -20256,6 +20611,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -20279,6 +20635,7 @@ ] }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -20302,6 +20659,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -20580,6 +20938,13 @@ }, "predicate": { "description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'", + "enum": [ + "biolink:author", + "biolink:contributor", + "biolink:editor", + "biolink:provider", + "biolink:publisher" + ], "type": "string" }, "primary_knowledge_source": { @@ -20748,7 +21113,7 @@ }, "CorrelatedGeneToDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a gene (or gene product) and a disease for which the gene is statistically correlated with the disease rather than asserted as causal. Such associations typically derive from GWAS, co-occurrence analyses, or other statistical methods, and are annotated with scores such as a z-score or a diseases confidence score.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -20947,11 +21312,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -21038,6 +21400,15 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:biomarker_for", + "biolink:coexpressed_with", + "biolink:correlated_with", + "biolink:has_biomarker", + "biolink:negatively_correlated_with", + "biolink:occurs_together_in_literature_with", + "biolink:positively_correlated_with" + ], "type": "string" }, "primary_knowledge_source": { @@ -21113,11 +21484,8 @@ "description": "gene in which variation is shown to correlate with the disease." }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -21283,6 +21651,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -21324,6 +21693,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -21347,6 +21717,7 @@ ] }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -21370,6 +21741,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -21433,6 +21805,7 @@ ] }, "distribution_download_url": { + "description": "A URL from which a specific distribution (serialization or format) of a dataset may be directly downloaded; corresponds to dcat:downloadURL specialised for the dataset distribution domain.", "type": [ "string", "null" @@ -21449,6 +21822,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -21490,6 +21864,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -21513,6 +21888,7 @@ ] }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -21536,6 +21912,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -21609,6 +21986,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -21650,6 +22028,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -21673,18 +22052,21 @@ ] }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" ] }, "source_logo": { + "description": "A URL referencing an image that serves as the visual logo of a data source.", "type": [ "string", "null" ] }, "source_web_page": { + "description": "A URL of a web page that documents or serves as the landing page for a data source.", "type": [ "string", "null" @@ -21708,6 +22090,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -21781,6 +22164,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -21804,12 +22188,14 @@ ] }, "has_dataset": { + "description": "Links a dataset version to the underlying dataset that it is a version of.", "type": [ "string", "null" ] }, "has_distribution": { + "description": "Links a dataset version to one of its dataset distributions (a specific representation or serialization of the dataset).", "type": [ "string", "null" @@ -21827,6 +22213,7 @@ ] }, "ingest_date": { + "description": "The date on which a dataset version was ingested into the local knowledge graph or downstream data system; a specialization of dct:issued for the ingestion context.", "type": [ "string", "null" @@ -21840,6 +22227,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -21863,6 +22251,7 @@ ] }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -21886,6 +22275,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -22020,6 +22410,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -22154,6 +22545,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -22181,7 +22573,7 @@ "type": "object" }, "DirectionQualifierEnum": { - "description": "", + "description": "An enumeration of values that qualify a change or effect by its direction, i.e., whether the referenced quantity or activity is increased (including up-regulated) or decreased (including down-regulated).", "enum": [ "increased", "upregulated", @@ -22193,7 +22585,7 @@ }, "Disease": { "additionalProperties": false, - "description": "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.", + "description": "A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22323,6 +22715,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -22601,6 +22994,11 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:associated_with_resistance_to", + "biolink:associated_with_response_to", + "biolink:associated_with_sensitivity_to" + ], "type": "string" }, "primary_knowledge_source": { @@ -22777,7 +23175,7 @@ }, "DiseaseOrPhenotypicFeature": { "additionalProperties": false, - "description": "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature.", + "description": "A disease or an individual phenotypic feature, grouped as a single class to accommodate source vocabularies and assertions that do not distinguish the two. Prefer the more specific subclasses disease or phenotypic feature when the distinction is known.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22907,6 +23305,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -22935,7 +23334,7 @@ }, "DiseaseOrPhenotypicFeatureExposure": { "additionalProperties": false, - "description": "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer.", + "description": "A disease or phenotypic feature state, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome,.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23106,6 +23505,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -23390,6 +23790,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:has_mode_of_inheritance" + ], "type": "string" }, "primary_knowledge_source": { @@ -24605,11 +25008,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -24785,11 +25185,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -24899,7 +25296,7 @@ "description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -25038,14 +25435,14 @@ ] }, "is_supplement": { - "description": "", + "description": "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food.", "type": [ "string", "null" ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -25103,13 +25500,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -25137,7 +25535,7 @@ "type": "object" }, "DrugAvailabilityEnum": { - "description": "", + "description": "An enumeration describing how a drug or chemical entity may be obtained, distinguishing products that are available over the counter from those that require a prescription.", "enum": [ "over_the_counter", "prescription" @@ -25146,7 +25544,7 @@ "type": "string" }, "DrugDeliveryEnum": { - "description": "", + "description": "An enumeration of routes by which a drug is administered or delivered to a patient, including inhalation, oral, transdermal absorption, and various forms of injection (intravenous, subcutaneous, intramuscular).", "enum": [ "inhalation", "oral", @@ -25342,6 +25740,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -25425,6 +25824,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -25476,6 +25876,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -25526,6 +25927,7 @@ "type": "array" }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -25556,6 +25958,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -26194,6 +26597,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -26221,7 +26625,7 @@ "type": "object" }, "DruggableGeneCategoryEnum": { - "description": "", + "description": "An enumeration of druggability categories for gene targets as defined by the IDG (Illuminating the Druggable Genome) / Pharos target development level classification: Tclin (targets of approved drugs), Tchem (targets with potent bioactives), Tbio (targets with biological knowledge), and Tdark (poorly characterized targets).", "enum": [ "tclin", "tbio", @@ -26233,7 +26637,7 @@ }, "DruggableGeneToDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a gene (or gene product) and a disease in which the gene is classified by its druggability (e.g., via the IDG/Pharos target development-level tiers).", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -26443,11 +26847,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -26534,7 +26935,10 @@ }, "predicate": { "$ref": "#/$defs/GeneToDiseasePredicateEnum", - "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" + "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "target_for" + ] }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", @@ -26721,13 +27125,13 @@ }, "Edge": { "additionalProperties": false, - "description": "An edge in a KGX graph, will be superclass for association", + "description": "A generic edge in a KGX-formatted knowledge graph, representing a directed relationship between a subject node and an object node qualified by a predicate. This class serves as the structural superclass for `association` in Biolink, providing the minimal KGX-compliant contract (subject, predicate, object, and associated metadata) that any biolink relationship participating in a knowledge graph must satisfy.", "title": "Edge", "type": "object" }, "EntityToDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between any entity and a disease, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases.", "properties": { "FDA_regulatory_approvals": { "description": "Numbers that identify specific drug applications. Each drug can have multiple approval numbers (for example, as seen with ranitidine having both ANADA200536 and ANDA200536).", @@ -27170,7 +27574,7 @@ }, "EntityToPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between any entity and a phenotypic feature, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases.", "properties": { "FDA_regulatory_approvals": { "description": "Numbers that identify specific drug applications. Each drug can have multiple approval numbers (for example, as seen with ranitidine having both ANADA200536 and ANDA200536).", @@ -27784,6 +28188,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -27812,7 +28217,7 @@ }, "EnvironmentalFeature": { "additionalProperties": false, - "description": "", + "description": "A system or entity in the natural environment that has the disposition to environ one or more material entities.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -27918,6 +28323,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -27946,10 +28352,10 @@ }, "EnvironmentalFoodContaminant": { "additionalProperties": false, - "description": "", + "description": "Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate foodstuffs during their production, transportation or storage.", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -28080,7 +28486,7 @@ ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -28138,13 +28544,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -28173,7 +28580,7 @@ }, "EnvironmentalProcess": { "additionalProperties": false, - "description": "", + "description": "A process that occurs within or involves the components of an environmental system.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -28279,6 +28686,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -28419,6 +28827,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -28492,6 +28901,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -28533,6 +28943,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -28556,6 +28967,7 @@ ] }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -28579,6 +28991,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -28713,6 +29126,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -28864,6 +29278,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -29481,6 +29896,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -30153,11 +30569,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -30326,11 +30739,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -30448,10 +30858,10 @@ }, "Food": { "additionalProperties": false, - "description": "A substance consumed by a living organism as a source of nutrition", + "description": "A substance of plant, animal, or artificial origin consumed by a living organism to provide essential nutrients, energy, and support growth and the processes of life, or to satisfy other health needs or provide a social or organoleptic experience.", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -30590,14 +31000,14 @@ ] }, "is_supplement": { - "description": "", + "description": "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food.", "type": [ "string", "null" ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -30655,13 +31065,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -30690,10 +31101,10 @@ }, "FoodAdditive": { "additionalProperties": false, - "description": "", + "description": "Any substance which is added to food to preserve or enhance its flavour and/or appearance.", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -30824,7 +31235,7 @@ ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -30882,13 +31293,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -31335,7 +31747,7 @@ }, "Fungus": { "additionalProperties": false, - "description": "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds).", + "description": "", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -31458,6 +31870,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -31623,6 +32036,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -31699,7 +32113,7 @@ }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", - "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" + "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", @@ -31866,6 +32280,7 @@ ] }, "object_context_qualifier": { + "description": "A qualifier describing the context in which the object of an association holds.", "type": [ "string", "null" @@ -31909,7 +32324,7 @@ }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement)." }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", @@ -31941,6 +32356,15 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:affects", + "biolink:ameliorates_condition", + "biolink:disrupts", + "biolink:exacerbates_condition", + "biolink:has_adverse_event", + "biolink:has_side_effect", + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -31962,6 +32386,9 @@ }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", + "enum": [ + "biolink:causes" + ], "type": [ "string", "null" @@ -32019,7 +32446,7 @@ ] }, "subject": { - "$ref": "#/$defs/GeneOrGeneProduct", + "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." }, "subject_aspect_qualifier": { @@ -32054,6 +32481,7 @@ ] }, "subject_context_qualifier": { + "description": "A qualifier describing the context in which the subject of an association holds.", "type": [ "string", "null" @@ -32100,7 +32528,7 @@ }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement)." }, "supporting_text": { "description": "The segment of text from a document that supports the mined assertion.", @@ -32152,7 +32580,7 @@ }, "GeneAsAModelOfDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association in which a gene (e.g., a model-organism ortholog of a known disease gene) serves as a model of a human disease - for example, because mutants of the gene recapitulate core features of the disease.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -32358,11 +32786,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -32449,7 +32874,10 @@ }, "predicate": { "$ref": "#/$defs/GeneToDiseasePredicateEnum", - "description": "The relationship to the disease" + "description": "The relationship to the disease", + "enum": [ + "model_of" + ] }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", @@ -32735,7 +33163,7 @@ ] }, "name": { - "description": "A human-readable name for an attribute or entity.", + "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", "type": [ "string", "null" @@ -32769,6 +33197,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -32963,8 +33392,8 @@ ] }, "object": { - "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", - "type": "string" + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -33047,6 +33476,15 @@ }, "predicate": { "description": "membership of a gene or gene product, or strict subset relationship gene family, in the given gene family.", + "enum": [ + "biolink:has_active_ingredient", + "biolink:has_excipient", + "biolink:has_food_component", + "biolink:has_nutrient", + "biolink:has_part", + "biolink:has_plasma_membrane_part", + "biolink:has_variant_part" + ], "type": "string" }, "primary_knowledge_source": { @@ -33215,7 +33653,7 @@ }, "GeneHasVariantThatContributesToDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "A gene-to-disease association that is asserted on the grounds that the gene harbours a sequence variant that contributes to the disease. Qualifies the gene with the form or variant that underlies the contribution.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -33491,7 +33929,11 @@ }, "predicate": { "$ref": "#/$defs/GeneToDiseasePredicateEnum", - "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" + "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "causes", + "contributes_to" + ] }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", @@ -33673,7 +34115,7 @@ "type": "object" }, "GeneOrGeneProductOrChemicalEntityAspectEnum": { - "description": "", + "description": "An enumeration used as a qualifier to indicate the specific aspect of a gene, gene product, or chemical entity that is affected or measured in an association. Values cover activity and abundance (expression, synthesis, degradation, stability, localization, transport), molecular interactions, and a wide range of molecular modifications such as phosphorylation, methylation, acetylation, ubiquitination, and other post-translational or chemical modifications.", "enum": [ "activity_or_abundance", "abundance", @@ -33737,7 +34179,7 @@ "type": "string" }, "GeneOrGeneProductOrChemicalPartQualifierEnum": { - "description": "", + "description": "An enumeration used as a qualifier to indicate a particular structural or functional part of a gene, gene product, or chemical (e.g., 3' UTR, 5' UTR, poly-A tail, promoter, enhancer, exon, or intron).", "enum": [ "3_prime_utr", "5_prime_utr", @@ -34420,6 +34862,17 @@ }, "predicate": { "description": "participation of a gene or gene product or gene family in a given biological process or activity (e.g., gene product participates in biological process; gene catalyzes molecular activity; gene family is actively involved in a pathway).", + "enum": [ + "biolink:actively_involved_in", + "biolink:capable_of", + "biolink:catalyzes", + "biolink:consumed_by", + "biolink:enables", + "biolink:is_input_of", + "biolink:is_output_of", + "biolink:is_substrate_of", + "biolink:participates_in" + ], "type": "string" }, "primary_knowledge_source": { @@ -34754,7 +35207,7 @@ ] }, "object": { - "$ref": "#/$defs/GeneOrGeneProduct", + "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." }, "object_aspect_qualifier": { @@ -34846,6 +35299,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -34867,6 +35323,9 @@ }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", + "enum": [ + "biolink:causes" + ], "type": "string" }, "qualifier": { @@ -34921,7 +35380,7 @@ ] }, "subject": { - "$ref": "#/$defs/GeneOrGeneProduct", + "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." }, "subject_category": { @@ -35028,7 +35487,7 @@ }, "GeneToDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a gene or gene product and a disease, where variation in the gene is correlated with the disease.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -35753,6 +36212,9 @@ }, "predicate": { "description": "expression relationship", + "enum": [ + "biolink:expressed_in" + ], "type": "string" }, "primary_knowledge_source": { @@ -36199,6 +36661,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:coexpressed_with" + ], "type": "string" }, "primary_knowledge_source": { @@ -36631,6 +37096,9 @@ }, "predicate": { "description": "membership of the gene in the given gene family.", + "enum": [ + "biolink:member_of" + ], "type": "string" }, "primary_knowledge_source": { @@ -37049,6 +37517,12 @@ }, "predicate": { "description": "homology relationship type", + "enum": [ + "biolink:homologous_to", + "biolink:orthologous_to", + "biolink:paralogous_to", + "biolink:xenologous_to" + ], "type": "string" }, "primary_knowledge_source": { @@ -37467,6 +37941,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:has_gene_product" + ], "type": "string" }, "primary_knowledge_source": { @@ -37635,7 +38112,7 @@ }, "GeneToGoTermAssociation": { "additionalProperties": false, - "description": "", + "description": "A functional association between a gene (or gene product or macromolecular complex) and a Gene Ontology (GO) term describing the molecular function, biological process, or cellular component in which it participates.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -38471,7 +38948,7 @@ }, "GeneToPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a gene or gene product and a phenotypic feature, where variation in the gene is correlated with the phenotypic feature.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -38690,11 +39167,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -38986,7 +39460,7 @@ }, "GeneticInheritance": { "additionalProperties": false, - "description": "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.", + "description": "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -39109,6 +39583,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -39267,6 +39742,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -39500,6 +39976,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -39793,6 +40270,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:has_sequence_location" + ], "type": "string" }, "primary_knowledge_source": { @@ -40033,6 +40513,7 @@ ] }, "has_zygosity": { + "description": "The zygosity characterising a genotype or nucleic acid entity at a particular locus.", "type": [ "string", "null" @@ -40108,6 +40589,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -40136,7 +40618,7 @@ }, "GenotypeAsAModelOfDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association in which a genotype serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -40320,11 +40802,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -40411,6 +40890,9 @@ }, "predicate": { "description": "The relationship to the disease", + "enum": [ + "biolink:model_of" + ], "type": "string" }, "primary_knowledge_source": { @@ -40486,11 +40968,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -40597,7 +41076,7 @@ }, "GenotypeToDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a genotype and a disease, in which the genotype (typically a combination of alleles at one or more loci) is linked to the disease state.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -40781,11 +41260,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -40872,6 +41348,9 @@ }, "predicate": { "description": "E.g. is pathogenic for", + "enum": [ + "biolink:related_condition" + ], "type": "string" }, "primary_knowledge_source": { @@ -40947,11 +41426,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -41726,6 +42202,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:has_variant_part" + ], "type": "string" }, "primary_knowledge_source": { @@ -42105,11 +42584,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -42196,6 +42672,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:has_phenotype" + ], "type": "string" }, "primary_knowledge_source": { @@ -42278,11 +42757,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -42934,6 +43410,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -43134,6 +43611,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -43282,6 +43760,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -43438,6 +43917,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -43466,7 +43946,7 @@ }, "GrossAnatomicalStructure": { "additionalProperties": false, - "description": "", + "description": "An anatomical structure that has more than one cell as a part.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -43589,6 +44069,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -43747,6 +44228,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -43775,7 +44257,7 @@ }, "Hospitalization": { "additionalProperties": false, - "description": "", + "description": "The admission and care of a patient in a hospital for observation, diagnosis, or treatment.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -43881,6 +44363,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -43915,7 +44398,7 @@ }, "Human": { "additionalProperties": false, - "description": "A member of the the species Homo sapiens.", + "description": "", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -44038,6 +44521,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -44231,6 +44715,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -44259,7 +44744,7 @@ }, "IndividualOrganism": { "additionalProperties": false, - "description": "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576", + "description": "An instance of an organism. For example, Charles Darwin, my pet cat.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -44382,6 +44867,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -44660,6 +45146,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:mentions" + ], "type": "string" }, "primary_knowledge_source": { @@ -44828,7 +45317,7 @@ }, "Invertebrate": { "additionalProperties": false, - "description": "An animal lacking a vertebral column. This group consists of 98% of all animal species.", + "description": "", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -44951,6 +45440,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -45034,6 +45524,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -45099,6 +45590,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -45153,6 +45645,7 @@ "type": "string" }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -45183,6 +45676,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -45220,7 +45714,7 @@ }, "KnowledgeGraph": { "additionalProperties": false, - "description": "A knowledge graph represented in KGX format", + "description": "A container representing a knowledge graph serialized in KGX (Knowledge Graph Exchange) format. A KnowledgeGraph aggregates a collection of nodes (entities) and edges (relationships between entities) conforming to the KGX specification, enabling interoperable exchange of biomedical knowledge graphs across tools and systems in the Biolink ecosystem.", "properties": { "edges": { "description": "A list of associations between two entities.", @@ -46302,7 +46796,7 @@ "type": "object" }, "KnowledgeLevelEnum": { - "description": "", + "description": "An enumeration characterizing the type of knowledge expressed in a statement and the kind of evidence and reasoning that supports it, as defined by the Translator Knowledge Level / Agent Type (KL/AT) standard. Values include knowledge assertion, logical entailment, prediction, statistical association, text co-occurrence, direct observation, and not-provided.", "enum": [ "knowledge_assertion", "logical_entailment", @@ -46440,6 +46934,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -46574,6 +47069,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -46601,7 +47097,7 @@ "type": "object" }, "LogicalInterpretationEnum": { - "description": "", + "description": "An enumeration of logical interpretations that can be applied to a triple to indicate whether the relation should be read as existential on both sides (some-some), universal-existential (all-some), or its inverse (inverse all-some).", "enum": [ "some_some", "all_some", @@ -46735,6 +47231,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -47013,6 +47510,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:has_substrate" + ], "type": "string" }, "primary_knowledge_source": { @@ -48456,7 +48956,7 @@ }, "Mammal": { "additionalProperties": false, - "description": "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex", + "description": "", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -48579,6 +49079,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -48713,6 +49214,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -48991,6 +49493,10 @@ }, "predicate": { "description": "derivation relationship", + "enum": [ + "biolink:derives_from", + "biolink:is_metabolite_of" + ], "type": "string" }, "primary_knowledge_source": { @@ -49608,7 +50114,7 @@ }, "MicroRNA": { "additionalProperties": false, - "description": "", + "description": "A small (~22 nucleotide) RNA molecule that is the endogenous transcript of a miRNA gene. Produced from precursor molecules that form hairpin structures, which are processed (typically via the Dicer pathway) to yield a single miRNA molecule. miRNAs function by triggering cleavage of target molecules or acting as translational repressors.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -49731,6 +50237,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -49912,6 +50419,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -51026,6 +51534,15 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:food_component_of", + "biolink:is_active_ingredient_of", + "biolink:is_excipient_of", + "biolink:nutrient_of", + "biolink:part_of", + "biolink:plasma_membrane_part_of", + "biolink:variant_part_of" + ], "type": "string" }, "primary_knowledge_source": { @@ -51197,7 +51714,7 @@ "description": "A molecular entity is a chemical entity composed of individual or covalently bonded atoms.", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -51335,7 +51852,7 @@ ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -51393,13 +51910,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -51431,7 +51949,7 @@ "description": "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -51570,14 +52088,14 @@ ] }, "is_supplement": { - "description": "", + "description": "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food.", "type": [ "string", "null" ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -51635,13 +52153,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -51782,6 +52301,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -51810,7 +52330,7 @@ }, "NamedThingAssociatedWithLikelihoodOfNamedThingAssociation": { "additionalProperties": false, - "description": "", + "description": "An association in which the subject entity is linked to the likelihood of the object entity occurring, manifesting, or being observed. Subject and object may each be qualified by aspect and context, and the association may be further qualified by a population context.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -51980,11 +52500,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -52014,6 +52531,7 @@ ] }, "object_context_qualifier": { + "description": "A qualifier describing the context in which the object of an association holds.", "type": [ "string", "null" @@ -52080,6 +52598,32 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:associated_with", + "biolink:associated_with_decreased_likelihood_of", + "biolink:associated_with_increased_likelihood_of", + "biolink:associated_with_likelihood_of", + "biolink:associated_with_resistance_to", + "biolink:associated_with_response_to", + "biolink:associated_with_sensitivity_to", + "biolink:biomarker_for", + "biolink:coexpressed_with", + "biolink:condition_associated_with_gene", + "biolink:correlated_with", + "biolink:decreased_likelihood_associated_with", + "biolink:gene_associated_with_condition", + "biolink:genetic_association", + "biolink:genetically_associated_with", + "biolink:has_biomarker", + "biolink:increased_likelihood_associated_with", + "biolink:likelihood_associated_with", + "biolink:negatively_correlated_with", + "biolink:occurs_together_in_literature_with", + "biolink:positively_correlated_with", + "biolink:resistance_associated_with", + "biolink:response_associated_with", + "biolink:sensitivity_associated_with" + ], "type": "string" }, "primary_knowledge_source": { @@ -52148,11 +52692,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -52182,6 +52723,7 @@ ] }, "subject_context_qualifier": { + "description": "A qualifier describing the context in which the subject of an association holds.", "type": [ "string", "null" @@ -52261,13 +52803,13 @@ }, "Node": { "additionalProperties": false, - "description": "A node in a KGX graph, will be superclass for named thing", + "description": "A generic node in a KGX-formatted knowledge graph, representing a single entity or concept with a unique identifier. This class serves as the structural superclass for `named thing` in Biolink, providing the minimal KGX-compliant contract (identifier, category, etc.) that any biolink entity participating in a knowledge graph must satisfy.", "title": "Node", "type": "object" }, "NoncodingRNAProduct": { "additionalProperties": false, - "description": "", + "description": "An RNA transcript that does not encode for a protein rather the RNA molecule is the functional gene product.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -52390,6 +52932,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -52421,7 +52964,7 @@ "description": "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -52583,7 +53126,7 @@ ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -52641,13 +53184,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -52676,7 +53220,7 @@ }, "NucleicAcidSequenceMotif": { "additionalProperties": false, - "description": "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences.", + "description": "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. consensus sequences.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -52799,6 +53343,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -52827,7 +53372,7 @@ }, "NucleosomeModification": { "additionalProperties": false, - "description": "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.", + "description": "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -52957,6 +53502,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -53091,6 +53637,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -53246,6 +53793,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -53402,6 +53950,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -53485,6 +54034,7 @@ ] }, "has_taxonomic_rank": { + "description": "The taxonomic rank (e.g. species, genus, family, order, kingdom) assigned to an organism taxon.", "type": [ "string", "null" @@ -53543,6 +54093,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -53828,6 +54379,18 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:binds", + "biolink:directly_physically_interacts_with", + "biolink:gene_fusion_with", + "biolink:genetic_neighborhood_of", + "biolink:genetically_interacts_with", + "biolink:indirectly_physically_interacts_with", + "biolink:interacts_with", + "biolink:pharmacologically_interacts_with", + "biolink:physically_interacts_with", + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -54246,6 +54809,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:subclass_of" + ], "type": "string" }, "primary_knowledge_source": { @@ -54414,7 +54980,7 @@ }, "OrganismToOrganismAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between two individual organisms (e.g., symbiosis, parasitism, predation, or other inter-organism relationships).", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -54832,7 +55398,7 @@ }, "OrganismalEntityAsAModelOfDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association in which an organismal entity (e.g., a strain or breed) serves as a model of a disease, either because it has a natural predisposition to the disease or was bred or engineered specifically to recapitulate it.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -55016,11 +55582,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -55107,6 +55670,9 @@ }, "predicate": { "description": "The relationship to the disease", + "enum": [ + "biolink:model_of" + ], "type": "string" }, "primary_knowledge_source": { @@ -55182,11 +55748,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -55543,6 +56106,18 @@ }, "predicate": { "description": "interaction relationship type", + "enum": [ + "biolink:binds", + "biolink:directly_physically_interacts_with", + "biolink:gene_fusion_with", + "biolink:genetic_neighborhood_of", + "biolink:genetically_interacts_with", + "biolink:indirectly_physically_interacts_with", + "biolink:interacts_with", + "biolink:pharmacologically_interacts_with", + "biolink:physically_interacts_with", + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -55967,6 +56542,18 @@ }, "predicate": { "description": "interaction relationship type", + "enum": [ + "biolink:binds", + "biolink:directly_physically_interacts_with", + "biolink:gene_fusion_with", + "biolink:genetic_neighborhood_of", + "biolink:genetically_interacts_with", + "biolink:indirectly_physically_interacts_with", + "biolink:interacts_with", + "biolink:pharmacologically_interacts_with", + "biolink:physically_interacts_with", + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -56190,6 +56777,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -56241,6 +56829,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -56291,6 +56880,7 @@ "type": "array" }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -56321,6 +56911,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -56350,7 +56941,7 @@ }, "PathologicalAnatomicalExposure": { "additionalProperties": false, - "description": "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome.", + "description": "An abnormal anatomical structure, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -56521,6 +57112,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -56678,6 +57270,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -56859,6 +57452,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -56887,7 +57481,7 @@ }, "PathologicalProcessExposure": { "additionalProperties": false, - "description": "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease.", + "description": "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -57058,6 +57652,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -57092,7 +57687,7 @@ }, "Pathway": { "additionalProperties": false, - "description": "", + "description": "A hierarchical ordering of connected molecular reactions (steps) that represent a specific biological process, such as signaling or metabolism.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -57245,6 +57840,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -57389,6 +57985,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -57417,7 +58014,7 @@ }, "PhenotypicFeature": { "additionalProperties": false, - "description": "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.", + "description": "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual often resulting from the interaction of its genotype with its molecular and physical environment.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -57547,6 +58144,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -57575,7 +58173,7 @@ }, "PhenotypicFeatureToDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a phenotypic feature (sign or symptom) and a disease, where the phenotypic feature is a manifestation or clinical indicator of the disease.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -57786,11 +58384,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -57877,6 +58472,32 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:associated_with", + "biolink:associated_with_decreased_likelihood_of", + "biolink:associated_with_increased_likelihood_of", + "biolink:associated_with_likelihood_of", + "biolink:associated_with_resistance_to", + "biolink:associated_with_response_to", + "biolink:associated_with_sensitivity_to", + "biolink:biomarker_for", + "biolink:coexpressed_with", + "biolink:condition_associated_with_gene", + "biolink:correlated_with", + "biolink:decreased_likelihood_associated_with", + "biolink:gene_associated_with_condition", + "biolink:genetic_association", + "biolink:genetically_associated_with", + "biolink:has_biomarker", + "biolink:increased_likelihood_associated_with", + "biolink:likelihood_associated_with", + "biolink:negatively_correlated_with", + "biolink:occurs_together_in_literature_with", + "biolink:positively_correlated_with", + "biolink:resistance_associated_with", + "biolink:response_associated_with", + "biolink:sensitivity_associated_with" + ], "type": "string" }, "primary_knowledge_source": { @@ -57959,11 +58580,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -58281,11 +58899,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -58454,11 +59069,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -58565,7 +59177,7 @@ }, "PhenotypicQuality": { "additionalProperties": false, - "description": "A property of a phenotype", + "description": "A characteristic of a phenotype (e.g., weight, size, shape, color) that can be observed, measured, or compared across organisms or conditions.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -58692,6 +59304,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -58848,6 +59461,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -58983,6 +59597,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -59011,7 +59626,7 @@ }, "PhysiologicalProcess": { "additionalProperties": false, - "description": "", + "description": "A biological or chemical function within a living organism.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -59164,6 +59779,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -59298,6 +59914,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -59449,6 +60066,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -59600,6 +60218,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -59751,6 +60370,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -60197,7 +60817,7 @@ }, "PosttranslationalModification": { "additionalProperties": false, - "description": "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination.", + "description": "A chemical modification of a polypeptide or protein that occurs after translation, altering its structure, activity, localization, or interactions.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -60320,6 +60940,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -60372,7 +60993,7 @@ }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", - "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" + "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" }, "exact_match": { "description": "holds between two entities that have strictly equivalent meanings, with a high degree of confidence", @@ -60402,13 +61023,11 @@ ] }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_context_qualifier": { + "description": "A qualifier describing the context in which the object of an association holds.", "type": [ "string", "null" @@ -60433,7 +61052,7 @@ ] }, "object_part_qualifier": { - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement).", "type": [ "string", "null" @@ -60458,13 +61077,11 @@ ] }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_context_qualifier": { + "description": "A qualifier describing the context in which the subject of an association holds.", "type": [ "string", "null" @@ -60489,7 +61106,7 @@ ] }, "subject_part_qualifier": { - "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement).", + "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement).", "type": [ "string", "null" @@ -60559,6 +61176,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -60610,6 +61228,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -60660,6 +61279,7 @@ "type": "array" }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -60690,6 +61310,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -60825,6 +61446,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -61103,6 +61725,9 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -61274,7 +61899,7 @@ "description": "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing.", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -61413,14 +62038,14 @@ ] }, "is_supplement": { - "description": "", + "description": "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food.", "type": [ "string", "null" ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -61478,13 +62103,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -61636,6 +62262,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -61664,7 +62291,7 @@ }, "ProteinDomain": { "additionalProperties": false, - "description": "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.", + "description": "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -61797,6 +62424,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -61825,7 +62453,7 @@ }, "ProteinFamily": { "additionalProperties": false, - "description": "", + "description": "A set of proteins coding for diverse functions which, by virtue of their high degree of sequence similarity, are believed to have evolved from a single ancestral gene.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -61958,6 +62586,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -61986,7 +62615,7 @@ }, "ProteinIsoform": { "additionalProperties": false, - "description": "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/", + "description": "Represents a protein that is a specific isoform of the canonical or reference protein.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -62109,6 +62738,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -62137,7 +62767,7 @@ }, "Publication": { "additionalProperties": false, - "description": "Any \u2018published\u2019 piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP).", + "description": "Any \u2018published\u2019 piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope.", "properties": { "authors": { "description": "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.", @@ -62192,6 +62822,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -62243,6 +62874,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -62293,6 +62925,7 @@ "type": "array" }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -62323,6 +62956,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -62374,7 +63008,7 @@ }, "RNAProduct": { "additionalProperties": false, - "description": "", + "description": "High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds typically synthesized by a DNA- or RNA-dependent RNA polymerase that constitutes the product of a gene. Distinct in emphasis from `biolink:Transcript`, which denotes the informational output of transcription at the gene-model level rather than the chemical species itself.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -62497,6 +63131,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -62648,6 +63283,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -62675,7 +63311,7 @@ "type": "object" }, "ReactionDirectionEnum": { - "description": "", + "description": "An enumeration of possible directions for a biochemical reaction, indicating whether it proceeds left-to-right, right-to-left, is bidirectional (reversible), or has no net direction.", "enum": [ "left_to_right", "right_to_left", @@ -62686,7 +63322,7 @@ "type": "string" }, "ReactionSideEnum": { - "description": "", + "description": "An enumeration indicating on which side of a biochemical reaction a participant appears - the left-hand (reactant/substrate) side or the right-hand (product) side, as written.", "enum": [ "left", "right" @@ -62696,7 +63332,7 @@ }, "ReactionToCatalystAssociation": { "additionalProperties": false, - "description": "", + "description": "A specialization of reaction-to-participant association in which the participant is a gene or gene product (e.g., an enzyme) that catalyses the reaction.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -63136,7 +63772,7 @@ }, "ReactionToParticipantAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a biochemical reaction and a participating molecular entity, qualified by the stoichiometry, the side (reactant vs. product) on which the participant appears, and the direction of the reaction.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -63706,6 +64342,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -63864,6 +64501,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -64013,6 +64651,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -64040,7 +64679,7 @@ "type": "object" }, "ResearchPhaseEnum": { - "description": "", + "description": "An enumeration of research phases describing the stage of investigation for a drug or therapy, spanning preclinical research through clinical trial phases 1 through 4 (including phase 1/2 and phase 2/3 combinations).", "enum": [ "pre_clinical_research_phase", "clinical_trial_phase", @@ -64132,6 +64771,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -64173,6 +64813,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -64204,6 +64845,7 @@ "description": "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -64237,6 +64879,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -65272,6 +65915,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -65355,6 +65999,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -65420,6 +66065,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -65470,6 +66116,7 @@ "type": "array" }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -65664,6 +66311,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -65816,6 +66464,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -65847,7 +66496,7 @@ "description": "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).", "properties": { "available_from": { - "description": "", + "description": "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.", "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, @@ -65985,7 +66634,7 @@ ] }, "is_toxic": { - "description": "", + "description": "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.", "type": [ "boolean", "null" @@ -66043,13 +66692,14 @@ ] }, "trade_name": { - "description": "", + "description": "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.", "type": [ "string", "null" ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -66228,6 +66878,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -66383,6 +67034,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -66412,7 +67064,7 @@ }, "SocioeconomicExposure": { "additionalProperties": false, - "description": "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty).", + "description": "A socioeconomic exposure is a factor relating to social and financial status of an affected individual.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -66580,6 +67232,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -66764,6 +67417,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -66915,6 +67569,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -66988,6 +67643,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -67029,6 +67685,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -67052,6 +67709,7 @@ ] }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -67075,6 +67733,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -67241,6 +67900,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -67268,7 +67928,7 @@ }, "TaxonToTaxonAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between two organism taxa, capturing ecological or evolutionary relationships between the taxa (e.g., a host-pathogen relationship or shared habitat).", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -67865,6 +68525,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -68016,6 +68677,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -68592,6 +69254,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -68821,6 +69484,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -68849,7 +69513,7 @@ }, "VariantAsAModelOfDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association in which a sequence variant serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -69033,11 +69697,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -69124,6 +69785,9 @@ }, "predicate": { "description": "The relationship to the disease", + "enum": [ + "biolink:model_of" + ], "type": "string" }, "primary_knowledge_source": { @@ -69199,11 +69863,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -69310,7 +69971,7 @@ }, "VariantToDiseaseAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a sequence variant and a disease, in which the allele state of the variant is linked to the disease state.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -69494,11 +70155,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -69585,6 +70243,9 @@ }, "predicate": { "description": "E.g. is pathogenic for", + "enum": [ + "biolink:related_condition" + ], "type": "string" }, "primary_knowledge_source": { @@ -69660,11 +70321,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -70021,6 +70679,11 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:condition_associated_with_gene", + "biolink:gene_associated_with_condition", + "biolink:genetically_associated_with" + ], "type": "string" }, "primary_knowledge_source": { @@ -70453,6 +71116,15 @@ }, "predicate": { "description": "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats", + "enum": [ + "biolink:affects", + "biolink:ameliorates_condition", + "biolink:disrupts", + "biolink:exacerbates_condition", + "biolink:has_adverse_event", + "biolink:has_side_effect", + "biolink:regulates" + ], "type": "string" }, "primary_knowledge_source": { @@ -70635,7 +71307,7 @@ }, "VariantToPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a sequence variant and a phenotypic feature, in which the allele state of the variant is linked to the manifestation of the phenotype.", "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", @@ -70846,11 +71518,8 @@ "type": "string" }, "object_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -71019,11 +71688,8 @@ "type": "string" }, "subject_aspect_qualifier": { - "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum", + "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -71583,7 +72249,7 @@ }, "Vertebrate": { "additionalProperties": false, - "description": "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column.", + "description": "", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -71706,6 +72372,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -71857,6 +72524,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -71940,6 +72608,7 @@ ] }, "format": { + "description": "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.", "type": [ "string", "null" @@ -71991,6 +72660,7 @@ ] }, "license": { + "description": "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.", "type": [ "string", "null" @@ -72041,6 +72711,7 @@ "type": "array" }, "rights": { + "description": "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.", "type": [ "string", "null" @@ -72071,6 +72742,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, @@ -72100,7 +72772,7 @@ }, "Zygosity": { "additionalProperties": false, - "description": "", + "description": "An allelic state describing the degree of similarity between features at a single locus, specifically whether alleles at the same location on paired chromosomes are identical or different.", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -72227,6 +72899,7 @@ ] }, "type": { + "description": "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance.", "items": { "type": "string" }, diff --git a/project/owl/biolink_model.owl.ttl b/project/owl/biolink_model.owl.ttl index 6f67ee8bd..43d9755c4 100644 --- a/project/owl/biolink_model.owl.ttl +++ b/project/owl/biolink_model.owl.ttl @@ -105,7 +105,7 @@ biolink:DiseaseOrPhenotypicFeatureOutcome a owl:Class ; biolink:Edge a owl:Class ; rdfs:label "Edge" ; rdfs:subClassOf linkml:ClassDefinition ; - skos:definition "An edge in a KGX graph, will be superclass for association" ; + skos:definition "A generic edge in a KGX-formatted knowledge graph, representing a directed relationship between a subject node and an object node qualified by a predicate. This class serves as the structural superclass for `association` in Biolink, providing the minimal KGX-compliant contract (subject, predicate, object, and associated metadata) that any biolink relationship participating in a knowledge graph must satisfy." ; skos:inScheme biolink: . biolink:EpidemiologicalOutcome a owl:Class ; @@ -133,12 +133,12 @@ biolink:KnowledgeGraph a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:Association ; owl:onProperty biolink:edges ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Entity ; - owl:onProperty biolink:nodes ], [ a owl:Restriction ; owl:allValuesFrom biolink:Association ; owl:onProperty biolink:edges ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Entity ; + owl:onProperty biolink:nodes ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:edges ], @@ -147,16 +147,16 @@ biolink:KnowledgeGraph a owl:Class ; owl:onProperty biolink:nodes ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:edges ], + owl:onProperty biolink:nodes ], [ a owl:Restriction ; owl:allValuesFrom biolink:Entity ; owl:onProperty biolink:nodes ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:nodes ], + owl:onProperty biolink:edges ], linkml:ClassDefinition ; - skos:definition "A knowledge graph is a structured representation of knowledge in the form of a graph, where nodes represent entities or concepts, and edges represent relationships between them. Knowledge graphs are used to organize and connect information from various sources, enabling better understanding, analysis, and reasoning about complex domains.", - "A knowledge graph represented in KGX format" ; + skos:definition "A container representing a knowledge graph serialized in KGX (Knowledge Graph Exchange) format. A KnowledgeGraph aggregates a collection of nodes (entities) and edges (relationships between entities) conforming to the KGX specification, enabling interoperable exchange of biomedical knowledge graphs across tools and systems in the Biolink ecosystem.", + "A knowledge graph is a structured representation of knowledge in the form of a graph, where nodes represent entities or concepts, and edges represent relationships between them. Knowledge graphs are used to organize and connect information from various sources, enabling better understanding, analysis, and reasoning about complex domains." ; skos:inScheme biolink: . biolink:MappingCollection a owl:Class ; @@ -168,7 +168,7 @@ biolink:MappingCollection a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:predicate_mappings ], linkml:ClassDefinition ; - skos:definition "A collection of deprecated mappings." ; + skos:definition "An abstract container class that holds a set of predicate mappings. Serves as a top-level root for documents that enumerate how third-party or deprecated predicates should be rewritten to Biolink predicates and their associated qualifiers." ; skos:inScheme biolink: . biolink:MortalityOutcome a owl:Class ; @@ -183,7 +183,7 @@ biolink:MortalityOutcome a owl:Class ; biolink:Node a owl:Class ; rdfs:label "Node" ; rdfs:subClassOf linkml:ClassDefinition ; - skos:definition "A node in a KGX graph, will be superclass for named thing" ; + skos:definition "A generic node in a KGX-formatted knowledge graph, representing a single entity or concept with a unique identifier. This class serves as the structural superclass for `named thing` in Biolink, providing the minimal KGX-compliant contract (identifier, category, etc.) that any biolink entity participating in a knowledge graph must satisfy." ; skos:inScheme biolink: . biolink:PathologicalAnatomicalOutcome a owl:Class ; @@ -243,6 +243,7 @@ biolink:animal_model_available_from a owl:ObjectProperty ; rdfs:label "animal model available from" ; rdfs:range biolink:DiseaseOrPhenotypicFeature ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "A resource (such as a model organism database) from which an animal model representing the given disease or phenotypic feature may be obtained." ; skos:inScheme biolink: . biolink:binds a owl:DatatypeProperty, @@ -275,6 +276,7 @@ biolink:broad_matches a owl:DatatypeProperty ; biolink:broad_synonym a owl:DatatypeProperty ; rdfs:label "broad synonym" ; rdfs:subPropertyOf biolink:synonym ; + skos:definition "An alternate label for an entity whose meaning is broader (more general) than the primary label but is still useful as a lexical alternative." ; skos:exactMatch OIO:hasBroadSynonym ; skos:inScheme biolink: . @@ -523,6 +525,7 @@ biolink:created_with a owl:DatatypeProperty ; rdfs:label "created with" ; rdfs:domain biolink:Dataset ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "An identifier (typically a URL or CURIE) of the software tool, service, or pipeline used to create the dataset." ; skos:exactMatch pav:createdWith ; skos:inScheme biolink: . @@ -530,6 +533,7 @@ biolink:dataset_download_url a owl:DatatypeProperty ; rdfs:label "dataset download url" ; rdfs:domain biolink:Dataset ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "A URL from which the dataset itself may be directly downloaded specialised for the dataset domain." ; skos:inScheme biolink: . biolink:decreased_amount_in a owl:DatatypeProperty ; @@ -573,6 +577,7 @@ biolink:download_url a owl:DatatypeProperty ; rdfs:label "download url" ; rdfs:domain biolink:InformationContentEntity ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "A URL from which the information content entity may be directly downloaded in its native serialization." ; skos:inScheme biolink: . biolink:drug_rep_hub_disease_area a owl:DatatypeProperty ; @@ -598,6 +603,7 @@ biolink:exact_matches a owl:DatatypeProperty ; biolink:exact_synonym a owl:DatatypeProperty ; rdfs:label "exact synonym" ; rdfs:subPropertyOf biolink:synonym ; + skos:definition "An alternate label for an entity that denotes exactly the same meaning as the primary label and is interchangeable with it in all contexts." ; skos:exactMatch OIO:hasExactSynonym ; skos:inScheme biolink: . @@ -830,7 +836,7 @@ biolink:has_receptor a owl:ObjectProperty ; rdfs:domain biolink:ExposureEvent ; rdfs:range biolink:OrganismalEntity ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "the organism or organism part being exposed" ; + skos:definition "An entity that interacts with an exposure stimulus during an exposure event." ; skos:exactMatch ExO:0000001 ; skos:inScheme biolink: . @@ -860,7 +866,7 @@ biolink:has_stressor a owl:DatatypeProperty ; rdfs:domain biolink:ExposureEvent ; rdfs:subPropertyOf biolink:node_property ; skos:altLabel "has stimulus" ; - skos:definition "the process or entity that the receptor is being exposed to" ; + skos:definition "An agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure_receptor during an exposure event." ; skos:exactMatch ExO:0000000 ; skos:inScheme biolink: . @@ -949,6 +955,7 @@ biolink:indirectly_physically_interacts_with a owl:DatatypeProperty, owl:SymmetricProperty ; rdfs:label "indirectly physically interacts with" ; rdfs:subPropertyOf biolink:physically_interacts_with ; + skos:definition "Holds between two entities that physically interact by way of one or more intermediary entities, rather than through direct physical contact." ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -1122,6 +1129,7 @@ biolink:narrow_matches a owl:DatatypeProperty ; biolink:narrow_synonym a owl:DatatypeProperty ; rdfs:label "narrow synonym" ; rdfs:subPropertyOf biolink:synonym ; + skos:definition "An alternate label for an entity whose meaning is narrower (more specific) than the primary label, for example naming a particular sub-type." ; skos:exactMatch OIO:hasNarrowSynonym ; skos:inScheme biolink: . @@ -1266,6 +1274,7 @@ biolink:reaction_balanced a owl:DatatypeProperty ; rdfs:label "reaction balanced" ; rdfs:range xsd:boolean ; rdfs:subPropertyOf biolink:association_slot ; + skos:definition "Indicates whether a chemical reaction is stoichiometrically balanced, i.e. whether the conservation of atoms (and charge) holds between the reactants and the products." ; skos:inScheme biolink: . biolink:regulated_by a owl:ObjectProperty ; @@ -1280,6 +1289,7 @@ biolink:related_condition a owl:DatatypeProperty, owl:SymmetricProperty ; rdfs:label "related condition" ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; + skos:definition "Links a genotype or genetic variant to a condition (disease or phenotypic feature) that is associated with it." ; skos:exactMatch ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -1287,6 +1297,7 @@ biolink:related_condition a owl:DatatypeProperty, biolink:related_synonym a owl:DatatypeProperty ; rdfs:label "related synonym" ; rdfs:subPropertyOf biolink:synonym ; + skos:definition "An alternate label that is related to the primary label but is neither exactly synonymous nor cleanly broader or narrower; useful as a lexical pointer but not for strict equivalence. Corresponds to oboInOwl:hasRelatedSynonym." ; skos:exactMatch OIO:hasRelatedSynonym ; skos:inScheme biolink: . @@ -1341,6 +1352,7 @@ biolink:retrieved_on a owl:DatatypeProperty ; rdfs:domain biolink:Dataset ; rdfs:range xsd:date ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "The date on which a dataset was retrieved or harvested from its original source, following pav:retrievedOn." ; skos:exactMatch pav:retrievedOn ; skos:inScheme biolink: . @@ -1464,14 +1476,14 @@ biolink:supporting_study_cohort a owl:DatatypeProperty ; rdfs:label "supporting study cohort" ; rdfs:range xsd:string ; rdfs:subPropertyOf biolink:supporting_study_metadata ; - skos:definition "A description of a study population/cohort that was interrogated to provide evidence for the association (e.g. the inclusion and exclusion criteria)." ; + skos:definition "A description of a study population/cohort that was interrogated to provide evidence for the association." ; skos:inScheme biolink: . biolink:supporting_study_context a owl:DatatypeProperty ; rdfs:label "supporting study context" ; rdfs:range xsd:string ; rdfs:subPropertyOf biolink:supporting_study_metadata ; - skos:definition "A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue type, disease, etc.)." ; + skos:definition "A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system, tissue type, disease, etc.)." ; skos:inScheme biolink: . biolink:supporting_study_date_range a owl:DatatypeProperty ; @@ -1584,6 +1596,7 @@ biolink:version a owl:DatatypeProperty ; rdfs:subPropertyOf biolink:node_property ; skos:broadMatch pav:version, owl:versionInfo ; + skos:definition "A label identifying a particular release or edition of a dataset or resource, typically following a versioning scheme such as a semantic version string or a release date." ; skos:inScheme biolink: . biolink:version_of a owl:ObjectProperty ; @@ -1591,6 +1604,7 @@ biolink:version_of a owl:ObjectProperty ; rdfs:domain biolink:DatasetVersion ; rdfs:range biolink:DatasetSummary ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "Links a dataset version to the dataset summary of which it is a version, edition, or adaptation." ; skos:exactMatch dct:isVersionOf ; skos:inScheme biolink: . @@ -1649,6 +1663,7 @@ biolink:PathognomonicityQuantifier a owl:Class ; biolink:SensitivityQuantifier a owl:Class ; rdfs:label "sensitivity quantifier" ; rdfs:subClassOf biolink:RelationshipQuantifier ; + skos:definition "A relationship quantifier that measures the sensitivity of a relationship, such as the proportion of true positives correctly identified in a diagnostic or association context." ; skos:inScheme biolink: . biolink:active_in a owl:ObjectProperty ; @@ -1656,6 +1671,7 @@ biolink:active_in a owl:ObjectProperty ; rdfs:domain biolink:GeneOrGeneProduct ; rdfs:range biolink:CellularComponent ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; + skos:definition "Holds between a gene or gene product and a cellular component in which it carries out its molecular function." ; skos:exactMatch RO:0002432 ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -1673,6 +1689,7 @@ biolink:acts_upstream_of_negative_effect a owl:ObjectProperty ; rdfs:domain biolink:GeneOrGeneProduct ; rdfs:range biolink:BiologicalProcess ; rdfs:subPropertyOf biolink:acts_upstream_of ; + skos:definition "Holds between a gene or gene product and a biological process where the molecular function of the gene product is upstream of and has a negative (inhibiting or decreasing) effect on the execution of the process." ; skos:exactMatch RO:0004035 ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -1682,6 +1699,7 @@ biolink:acts_upstream_of_or_within_negative_effect a owl:ObjectProperty ; rdfs:domain biolink:GeneOrGeneProduct ; rdfs:range biolink:BiologicalProcess ; rdfs:subPropertyOf biolink:acts_upstream_of_or_within ; + skos:definition "Holds between a gene or gene product and a biological process when the gene product acts upstream of or within the process with a negative (inhibiting or decreasing) effect on its execution. Corresponds to RO:0004033." ; skos:exactMatch RO:0004033 ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -1691,6 +1709,7 @@ biolink:acts_upstream_of_or_within_positive_effect a owl:ObjectProperty ; rdfs:domain biolink:GeneOrGeneProduct ; rdfs:range biolink:BiologicalProcess ; rdfs:subPropertyOf biolink:acts_upstream_of_or_within ; + skos:definition "Holds between a gene or gene product and a biological process when the gene product acts upstream of or within the process with a positive (activating or increasing) effect on its execution. Corresponds to RO:0004032." ; skos:exactMatch RO:0004032 ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -1700,6 +1719,7 @@ biolink:acts_upstream_of_positive_effect a owl:ObjectProperty ; rdfs:domain biolink:GeneOrGeneProduct ; rdfs:range biolink:BiologicalProcess ; rdfs:subPropertyOf biolink:acts_upstream_of ; + skos:definition "Holds between a gene or gene product and a biological process where the molecular function of the gene product is upstream of and has a positive (activating or increasing) effect on the execution of the process." ; skos:exactMatch RO:0004034 ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -1730,7 +1750,7 @@ biolink:applied_to_treat a owl:ObjectProperty ; "given to treat", "used to treat" ; skos:definition "Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity was actually taken by one or more patients with the intent of treating the condition." ; - skos:editorialNote "This predicate is used simply to report observations of use in the real world, and is agnostic to whether the treatment is approved for or might be effective in treating the condition. The treatment could be taken by a patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS where patients directly report the condition for which they took a drug, or statements from a database cataloging instances of off-label prescription of drugs for specific conditions (e.g. here, here, here)." ; + skos:editorialNote "This predicate is used simply to report observations of use in the real world, and is agnostic to whether the treatment is approved for or might be effective in treating the condition. The treatment could be taken by a patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS where patients directly report the condition for which they took a drug, or statements from a database cataloging instances of off-label prescription of drugs for specific conditions." ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -1819,6 +1839,7 @@ biolink:capable_of a owl:ObjectProperty ; biolink:catalyzes a owl:DatatypeProperty ; rdfs:label "catalyzes" ; rdfs:subPropertyOf biolink:participates_in ; + skos:definition "Holds between a macromolecular machine (typically an enzyme or ribozyme) and a biochemical reaction or process whose rate it accelerates, without itself being consumed, by lowering the activation energy." ; skos:exactMatch RO:0002327 ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -1864,7 +1885,7 @@ biolink:close_match a owl:DatatypeProperty, owl:SymmetricProperty ; rdfs:label "close match" ; rdfs:subPropertyOf biolink:related_to_at_concept_level ; - skos:definition "a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives (e.g. drug as a type of chemical entity versus drug as a type of role borne by a chemical entity)." ; + skos:definition "a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives." ; skos:exactMatch skos:closeMatch, SEMMEDDB:same_as ; skos:inScheme biolink: ; @@ -1889,6 +1910,7 @@ biolink:consumes a owl:ObjectProperty ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:has_input ; + skos:definition "Holds between a process and an entity that is taken in and depleted by the process; for example a metabolite consumed in a biochemical reaction." ; skos:inScheme biolink: ; skos:narrowMatch RO:0004009 ; biolink:canonical_predicate true . @@ -1915,7 +1937,7 @@ biolink:dataset_count a owl:DatatypeProperty ; rdfs:label "dataset count" ; rdfs:range xsd:integer ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort." ; + skos:definition "The total number of instances in a dataset/cohort." ; skos:inScheme biolink: . biolink:decreases_amount_or_activity_of a owl:DatatypeProperty ; @@ -1929,7 +1951,7 @@ biolink:decreases_sensitivity_to a owl:ObjectProperty ; rdfs:domain biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:subPropertyOf biolink:affects_sensitivity_to ; - skos:definition "holds between two chemical entities or genes or gene products where the action or effect of one decreases the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other" ; + skos:definition "holds between two chemical entities or genes or gene products where the action or effect of one decreases the susceptibility/sensitivity of a biological entity or system to the other" ; skos:exactMatch CTD:decreases_response_to ; skos:inScheme biolink: ; skos:narrowMatch CTD:decreases_response_to_substance ; @@ -1953,6 +1975,7 @@ biolink:develops_from a owl:DatatypeProperty ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; skos:closeMatch FMA:develops_into, RO:0002203 ; + skos:definition "Holds between two entities where the first develops, by one or more developmental processes, from the second; for example a cell type developing from a precursor cell type or a tissue developing from an embryonic primordium. Corresponds to RO:0002202." ; skos:exactMatch , , FMA:develops_from, @@ -2134,6 +2157,7 @@ biolink:has_completed a owl:DatatypeProperty ; biolink:has_decreased_amount a owl:DatatypeProperty ; rdfs:label "has decreased amount" ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; + skos:definition "Holds between an entity and a component that is present at lower amount than in a reference state or sibling entity; used for comparative compositional statements." ; skos:inScheme biolink: ; skos:narrowMatch ; biolink:canonical_predicate true ; @@ -2152,6 +2176,7 @@ biolink:has_excipient a owl:ObjectProperty ; biolink:has_increased_amount a owl:DatatypeProperty ; rdfs:label "has increased amount" ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; + skos:definition "Holds between an entity and a component that is present at higher amount than in a reference state or sibling entity; used for comparative compositional statements." ; skos:inScheme biolink: ; skos:narrowMatch ; biolink:canonical_predicate true ; @@ -2274,6 +2299,7 @@ biolink:has_substrate a owl:ObjectProperty ; rdfs:domain biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:subPropertyOf biolink:has_participant ; + skos:definition "Holds between a biochemical reaction or catalytic process and a chemical entity that is acted upon (consumed or transformed) by that reaction." ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -2307,14 +2333,16 @@ biolink:increases_sensitivity_to a owl:ObjectProperty ; rdfs:domain biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:subPropertyOf biolink:affects_sensitivity_to ; - skos:definition "holds between two chemical entities or genes or gene products where the action or effect of one increases the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other" ; + skos:definition "holds between two chemical entities or genes or gene products where the action or effect of one increases the susceptibility/sensitivity of a biological entity or system to the other" ; skos:exactMatch CTD:increases_response_to ; skos:inScheme biolink: ; biolink:canonical_predicate true ; biolink:opposite_of "decreases sensitivity to" . -biolink:is_chemical_role_of a owl:DatatypeProperty ; +biolink:is_chemical_role_of a owl:ObjectProperty ; rdfs:label "is chemical role of" ; + rdfs:domain biolink:ChemicalRole ; + rdfs:range biolink:ChemicalEntity ; rdfs:subPropertyOf biolink:related_to_at_concept_level ; owl:inverseOf biolink:has_chemical_role ; skos:definition "Holds between a chemical role and a chemical entity that exhibits that role." ; @@ -2403,6 +2431,7 @@ biolink:is_synonymous_variant_of a owl:ObjectProperty ; biolink:lacks_part a owl:DatatypeProperty ; rdfs:label "lacks part" ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; + skos:definition "Holds between an entity and a component that is absent from it relative to a reference type; for example a cell type lacking a particular organelle or a protein lacking a particular domain. Corresponds to CL:lacks_part / PR:lacks_part." ; skos:exactMatch , ; skos:inScheme biolink: ; @@ -2528,7 +2557,7 @@ biolink:produces a owl:DatatypeProperty ; biolink:provider a owl:DatatypeProperty ; rdfs:label "provider" ; rdfs:subPropertyOf biolink:contributor ; - skos:definition "person, group, organization or project that provides a piece of information (e.g. a knowledge association)." ; + skos:definition "person, group, organization or project that provides a piece of information." ; skos:inScheme biolink: . biolink:publisher a owl:ObjectProperty ; @@ -2673,27 +2702,29 @@ biolink:was_tested_for_effect_on a owl:ObjectProperty ; os:AllSomeInterpretation a owl:Class ; rdfs:label "all_some" ; rdfs:subClassOf biolink:LogicalInterpretationEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A modifier on a triple that causes the triple to be interpreted as an all-some statement." . os:SomeSomeInterpretation a owl:Class ; rdfs:label "some_some" ; rdfs:subClassOf biolink:LogicalInterpretationEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A modifier on a triple that causes the triple to be interpreted as a some-some statement" . biolink:AccessibleDnaRegion a owl:Class ; rdfs:label "accessible dna region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], biolink:RegulatoryRegion ; skos:altLabel "atac-seq accessible region", "dnase-seq accessible region" ; @@ -2709,32 +2740,38 @@ biolink:AccessibleDnaRegion a owl:Class ; a owl:Class ; rdfs:label "pEC50" ; rdfs:subClassOf biolink:AffinityParameterEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Negative base 10 logarithm of the molar concentration of a chemical that produces a 50% excitation of a function" . a owl:Class ; rdfs:label "pIC50" ; rdfs:subClassOf biolink:AffinityParameterEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Negative base 10 logarithm of the the inhibitory concentration 50% (IC50) measures the concentration needed to block or inhibit a biological response." . a owl:Class ; rdfs:label "pKd" ; rdfs:subClassOf biolink:AffinityParameterEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Negative base 10 logarithm of the equilibrium dissociation constant (KD) which is a measure of the binding affinity and is defined as the ratio of koff to kon." . a owl:Class ; rdfs:label "pKi" ; rdfs:subClassOf biolink:AffinityParameterEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Negative base 10 logarithm of the equilibrium binding affinity for a ligand that reduces the activity of its binding partner. Ki represents the concentration at which the inhibitor ligand occupies 50% of the receptor sites when no competing ligand is present" . a owl:Class ; rdfs:label "pKoff" ; rdfs:subClassOf biolink:AffinityParameterEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Negative base 10 logarithm of the dissociation rate constant (koff) describes the rate at which they dissociate." . a owl:Class ; rdfs:label "pKon" ; rdfs:subClassOf biolink:AffinityParameterEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Negative base 10 logarithm of the association rate constant (Kon) describes the rate at which molecules bind to each other." . a owl:Class ; rdfs:label "pXC50" ; @@ -2744,37 +2781,48 @@ biolink:AccessibleDnaRegion a owl:Class ; a owl:Class ; rdfs:label "computational_model" ; rdfs:subClassOf biolink:AgentTypeEnum, - . + ; + skos:definition "An automated agent that generates knowledge statements (typically predictions) based on rules/logic explicitly encoded in an algorithm (e.g. heuristic models, supervised classifiers), or learned from patterns observed in data (e.g. ML models, unsupervised classifiers)." ; + skos:editorialNote "The bar is quite low relatively for what is considered to be a ‘computational model’ by our definition. Even agents/tools that apply simple rules or logic to the output of an ingest or analysis pipeline to allow for a stronger or more general conclusion to be stated can qualify an agent as a model. For example, an ingest pipeline that applies rules to its ingest of clinical trials data to create a 'treats' prediction edge when the source reports a drug to be in phase 2 or 3 trials represents a computational model because it is automatically drawing a stronger conclusion than the source reports, based on logic encoded in the ingest pipeline. Similarly, a data analysis pipeline that is extended with rules to automatically generate broader conclusions based on dataset-specific statistical correlations (e.g. create a 'treats' edge when the analysis reveals a drug-disease correlation in the data with statistical scores that meet a certain threshold), would also qualify as a computational model by our definition." . a owl:Class ; rdfs:label "data_analysis_pipeline" ; rdfs:subClassOf biolink:AgentTypeEnum, - . + ; + skos:definition "An automated agent that executes an analysis workflow over data and reports the direct results of the analysis. These typically report statistical associations/correlations between variables in the input dataset, and do not interpret/infer broader conclusions from associations the analysis reveals in the data." ; + skos:editorialNote "If an analysis pipeline includes any rules for generating broader conclusions based on the dataset-specific statistical correlations it calculates (e.g. create a 'treats' edge when the analysis reveals a drug-disease correlation in the data with statistical scores that meet a certain threshold) - we would consider this agent to be a Computational Model rather than just a Data Analysis Pipeline." . a owl:Class ; rdfs:label "image_processing_agent" ; rdfs:subClassOf biolink:AgentTypeEnum, - . + ; + skos:definition "An automated agent that processes images to generate textual statements of knowledge derived from the image and/or expressed in text the image depicts (e.g. via OCR)." . a owl:Class ; rdfs:label "manual_agent" ; rdfs:subClassOf biolink:AgentTypeEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A human agent who is responsible for generating a statement of knowledge. The human may utilize computationally generated information as evidence for the resulting knowledge, but the human is the one who ultimately interprets/reasons with this evidence to produce a statement of knowledge." . a owl:Class ; rdfs:label "manual_validation_of_automated_agent" ; rdfs:subClassOf biolink:AgentTypeEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A human agent reviews and validates/approves the veracity of knowledge that is initially generated by an automated agent." ; + skos:editorialNote "This term applies when a human was only involved in evaluating the veracity of a knowledge statement that was generated by an automated agent. It is important to indicate when such manual review has occurred, because it can give a user more confidence in an automated statement." . a owl:Class ; rdfs:label "not_provided" ; rdfs:subClassOf biolink:AgentTypeEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The agent type is not provided, typically because it cannot be determined from available information if the agent that generated the knowledge is manual or automated." . a owl:Class ; rdfs:label "text_mining_agent" ; rdfs:subClassOf biolink:AgentTypeEnum, - . + ; + skos:definition "An automated agent that uses Natural Language Processing to recognize concepts and/or relationships in text, and report them using formally encoded semantics (e.g. as an edge in a knowledge graph)." ; + skos:editorialNote "The original statement in the source text is typically made by a human / manual agent, but if a specific encoding of this knowledge is produced by a text-mining tool, it has an agent_type of 'text_mining_agent'. Examples of text mining agents include SemmedDB, and the Translator Text-Mining Knowledge Provider. Note that text-mining tools are prone to erroneous interpretation of concepts and relationships, and can fail to provide important details about the context in which the original knowledge was reported - so users should always consult the source text for a text-mined statement to assess its veracity and relevance." . biolink:AnatomicalEntityHasPartAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity has part anatomical entity association" ; @@ -2782,26 +2830,26 @@ biolink:AnatomicalEntityHasPartAnatomicalEntityAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], @@ -2812,32 +2860,32 @@ biolink:AnatomicalEntityHasPartAnatomicalEntityAssociation a owl:Class ; biolink:AnatomicalEntityPartOfAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity part of anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood, that is, the subject is a part of the object entity (the expected predicate is \"biolink:part_of\" or suitable predicate slots inheriting from it, i.e., \"biolink:plasma_membrane_part_of\", \"biolink:variant_part_of\", etc.). This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms." ; skos:inScheme biolink: . @@ -2846,15 +2894,15 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -2862,15 +2910,15 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; skos:inScheme biolink: . @@ -2878,62 +2926,74 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; a owl:Class ; rdfs:label "discovery_and_development_phase" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments." . a owl:Class ; rdfs:label "fda_accelerated_approval" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "When studying a new drug, it can sometimes take many years to learn whether a drug actually provides a real effect on how a patient survives, feels, or functions. A positive therapeutic effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”. Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. Using a surrogate endpoint enabled the FDA to approve these drugs faster. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval" . a owl:Class ; rdfs:label "fda_breakthrough_therapy" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Breakthrough Therapy designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy" . a owl:Class ; rdfs:label "fda_clinical_research_phase" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Clinical Research Phase. Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer." . a owl:Class ; rdfs:label "fda_clinical_research_phase_1" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase." . a owl:Class ; rdfs:label "fda_clinical_research_phase_2" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur." . a owl:Class ; rdfs:label "fda_clinical_research_phase_3" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions." . a owl:Class ; rdfs:label "fda_clinical_research_phase_4" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review." . a owl:Class ; rdfs:label "fda_fast_track" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Fast track is a process designed to facilitate the development, and expedite the review of drugs to treat serious conditions and fill an unmet medical need. The purpose is to get important new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track" . a owl:Class ; rdfs:label "fda_post_market_safety_review" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations." . a owl:Class ; rdfs:label "fda_priority_review" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving the drug review time and created a two-tiered system of review times – Standard Review and Priority Review. A Priority Review designation means FDA’s goal is to take action on an application within 6 months (compared to 10 months under standard review). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review" . a owl:Class ; rdfs:label "fda_review_phase_4" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "FDA Review" . a owl:Class ; rdfs:label "post_approval_withdrawal" ; @@ -2943,12 +3003,14 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; a owl:Class ; rdfs:label "preclinical_research_phase" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo." . a owl:Class ; rdfs:label "regular_fda_approval" ; rdfs:subClassOf biolink:ApprovalStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Regular FDA Approval. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations." . biolink:Bacterium a owl:Class ; rdfs:label "bacterium" ; @@ -2964,10 +3026,13 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Behavior ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Behavior ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -2978,9 +3043,6 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:BehavioralFeature ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; skos:inScheme biolink: . @@ -3009,11 +3071,8 @@ biolink:BehavioralExposure a owl:Class ; biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "biological process or activity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -3021,8 +3080,11 @@ biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation a owl:Class ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:subject ], @@ -3033,32 +3095,32 @@ biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation a owl:Class ; biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation a owl:Class ; rdfs:label "biological process or activity to biological process or activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcessOrActivity ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Classification relationship between biological processes or activities (e.g. coupling of two molecular activities; assignment of molecular activity to a pathway; implicating a pathway in a biological process; etc.)" ; skos:inScheme biolink: . @@ -3069,29 +3131,29 @@ biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation a owl:allValuesFrom biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProductOrGeneFamily ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrGeneFamily ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Relationship between a biological processor activity (e.g. molecular activity, biological process or pathway) to gene or gene product or gene family." ; skos:inScheme biolink: . @@ -3107,20 +3169,20 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], biolink:Publication ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; skos:inScheme biolink: . @@ -3132,40 +3194,40 @@ biolink:CaseToDiseaseAssociation a owl:Class ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:onset_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a Case (patient) and a Disease" ; skos:inScheme biolink: . @@ -3174,30 +3236,30 @@ biolink:CaseToGeneAssociation a owl:Class ; rdfs:label "case to gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; @@ -3209,6 +3271,9 @@ biolink:CaseToGeneAssociation a owl:Class ; biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "case to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; @@ -3216,21 +3281,18 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:negated ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:onset_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; + owl:minCardinality 0 ; owl:onProperty biolink:negated ], biolink:Association ; skos:definition "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; @@ -3239,28 +3301,25 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; biolink:CaseToVariantAssociation a owl:Class ; rdfs:label "case to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Zygosity ; - owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Zygosity ; + owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -3269,14 +3328,17 @@ biolink:CaseToVariantAssociation a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_zygosity ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Association between a Case and a Genetic Variant" ; skos:inScheme biolink: . @@ -3284,75 +3346,76 @@ biolink:CaseToVariantAssociation a owl:Class ; biolink:CausalGeneToDiseaseAssociation a owl:Class ; rdfs:label "causal gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( xsd:string [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^HP:\\d{7}$" ] ) ] ) ] ; - owl:onProperty biolink:allelic_requirement ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:allelic_requirement ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:allelic_requirement ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:allelic_requirement ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( xsd:string [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^HP:\\d{7}$" ] ) ] ) ] ; + owl:onProperty biolink:allelic_requirement ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], biolink:Association ; + skos:definition "An association between a gene and a disease where variation in the gene has been shown to have a causal role in the disease." ; skos:inScheme biolink: . a owl:Class ; @@ -3368,52 +3431,62 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "adduction" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A covalent binding mechanism in which a drug-protein adduct forms by the covalent binding of electrophilic drugs or their reactive metabolite(s) to a target protein." . a owl:Class ; rdfs:label "allosteric_antagonism" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An inhibition mechanism in which the effector binds to a receptor at an allosteric site and prevents activation by a positive allosteric modulator at that site." . a owl:Class ; rdfs:label "ampylation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A molecular modification involving the addition of an adenylyl (AMP) moiety to a substrate protein residue." . a owl:Class ; rdfs:label "antibody_agonism" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An agonism mechanism in which the effector is an antobody that binds and activates a receptor to mimic the effect of an endogenous ligand." . a owl:Class ; rdfs:label "antibody_inhibition" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An inhibition mechanism in which an antibody effector specifically binds to and interferes with the target." . a owl:Class ; rdfs:label "antisense_oligonucleotide_inhibition" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A negative modulation mechanism in which an antisense oligonucleotide effector prevents translation of a complementary mRNA sequence through binding and targeting it for degradation. Note that while this is called \"inhibition', it is not inhibition in the classic biochemical sense that requires a direct interaction between effector and target." . a owl:Class ; rdfs:label "atpase_activation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An activation mechanism in which the effector accelerates the intrinsic ATPase activity of a target protein, promoting the conversion of the active, ATP-bound form to the inactive, ADP-bound form, thereby terminating a signaling event. Note that this is a negative modulation mechanism because the target is the protein whose activity is attenuated through atpase activation." . a owl:Class ; rdfs:label "biased_agonism" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An agonism mechanism in which the effector binds to a receptor and activates certain signaling pathways while ignoring others, allowing it to produce a desired effect without unwanted side effects." . a owl:Class ; rdfs:label "binding" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction (typically non-covalent)." . a owl:Class ; rdfs:label "biphasic_allosteric_modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A mixed allosteric modulation mechanism that occurs when a chemical exerts an activating effect at lower concentrations, and an inhibitory effect at higher concentrations." . a owl:Class ; rdfs:label "carboxylation" ; @@ -3423,7 +3496,8 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "catalytic_activity" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism mediated by through the catalytic activity of the effector on the target." . a owl:Class ; rdfs:label "chaperone_mediated_stabilization" ; @@ -3433,32 +3507,38 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "chelation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which an effector binds to a metal ion target, reducing its availability/reactivity for further interactions." . a owl:Class ; rdfs:label "chemical_modification" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism mediated by a protein/complex effector altering a small molecule by modifying it or converting it to something else." . a owl:Class ; rdfs:label "cleavage" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which an effector promotes degeneration of the target protein through cleaving of the peptide bonds." . a owl:Class ; rdfs:label "cofactor" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A positive modulation mechanism in which the effector (usually some non-protein chemical compound or metallic ion) is required for a target enzyme's biological/catalytic activity." . a owl:Class ; rdfs:label "competitive_inhibition" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An inhibition mechanism in which the effector binds to a target molecule (such as an enzyme) and prevents the binding of a substrate (or another binding partner) and vice versa." . a owl:Class ; rdfs:label "crosslinking" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A covalent binding mechanism in which an effector induces cross-linking of target proteins or nucleic acids - covalently joining them into a rigid structure." . a owl:Class ; rdfs:label "de-ADP-ribosylation" ; @@ -3478,7 +3558,8 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "degradation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism that controls protein and cellular component levels through the regulated breakdown and recycling of molecules." . a owl:Class ; rdfs:label "demethylation" ; @@ -3498,7 +3579,8 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "destabilization" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which a chaperone molecule directly binds to a partially folded biosynthetic intermediate to stabilize the protein and allow it to complete the folding process to yield a functional protein." . a owl:Class ; rdfs:label "desumoylation" ; @@ -3513,32 +3595,38 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "disruption" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which an effector destabilizes or disrupts a protein complex, macromolecular assembly, cell membrane etc." . a owl:Class ; rdfs:label "disuphide_binding" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A covalent binding mechanism involving a covalent bond formed between two cysteine residues in or between proteins." . a owl:Class ; rdfs:label "exogenous_gene" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which a nucleic acid from an exogenous source acts as a substitute or supplement for a specific gene which is absent or has reduced function in an affected target/subject." . a owl:Class ; rdfs:label "exogenous_protein" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which a protein from an exogenous source acts as a substitute or supplement for a specific protein which is absent or has reduced function in an affected target/subject." . a owl:Class ; rdfs:label "feedback_inhibition" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An negative modulation mechanism in which the end product of a metabolic pathway inhibits an enzyme early in that same pathway, which stops the production of the final product when it's no longer needed." . a owl:Class ; rdfs:label "gating_inhibition" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An inhibition mechanism mediated by the transition of ion channels between their open (conducting) and closed (non-conducting) conformational states." . a owl:Class ; rdfs:label "glycosylation" ; @@ -3548,17 +3636,20 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "gtpase_activation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An activation mechanism in which the effector accelerates the intrinsic GTPase activity of a G-protein, promoting the conversion of the active, GTP-bound form to the inactive, GDP-bound form, thereby terminating a signaling event. Note that this is a negative modulation mechanism because the target is the G-protein whose activity is attenuated through gtpase activation." . a owl:Class ; rdfs:label "guanyl_nucleotide_exchange" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An activation mechanism in which the effector catalyzes the exchange of guanosine diphosphate (GDP) for guanosine triphosphate (GTP) in a guanine nucleotide-binding protein (G-protein)." . a owl:Class ; rdfs:label "hydrolysis" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which an effector cleaves its target through a chemical reaction where a molecule of water is used to break a bond." . a owl:Class ; rdfs:label "hydroxylation" ; @@ -3568,37 +3659,48 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "induction" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch DGIdb:inducer ; + skos:definition "A positive modulation mechanism in which the effector binds to and increases the activity/rate of an enzyme that processes drugs in the body." . a owl:Class ; rdfs:label "inverse_agonism" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch DGIdb:inverse_agonist, + CHEMBL.MECHANISM:inverse_agonist ; + skos:definition "An inhibition mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling." . a owl:Class ; rdfs:label "irreversible_inhibition" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An inhibition mechanism in which an effector permanently binds to a target, permanently disrupting its activity." . a owl:Class ; rdfs:label "isomerization" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism mediated by an effector that alters the isomeric conformation of a target." . a owl:Class ; rdfs:label "mixed_agonism" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An modulation mechanism in which the effector acts as both an agonist (activating a receptor) and an antagonist (blocking a receptor) at different receptor sites." . a owl:Class ; rdfs:label "molecular_channel_blockage" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An inhibition mechanism in which the effector binds to a molecular channel and prevents or reduces transport of ions through it." . a owl:Class ; rdfs:label "molecular_channel_opening" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch CHEMBL.MECHANISM:opener ; + skos:definition "An activation mechanism in which the effector binds to a molecular channel and facilitates transport of ions through it." . a owl:Class ; rdfs:label "monoubiquitination" ; @@ -3608,7 +3710,8 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "multitarget_modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which an effector achieves a physiological effect through simultaneous interaction with multiple gene targets." . a owl:Class ; rdfs:label "myristoylation" ; @@ -3623,32 +3726,40 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "negative_allosteric_modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch DGIdb:inhibitory_allosteric_modulator, + CHEMBL.MECHANISM:negative_allosteric_modulator ; + skos:definition "A noncompetitive inhibition mechanism in which the effector reduces or prevents the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand, and causing a conformational change that affects ligand binding." . a owl:Class ; rdfs:label "negative_gene_editing_modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A negative modulation mechanism in which the effector elicits the negative modulation of its target through a gene editing activity." . a owl:Class ; rdfs:label "non_competitive_antagonism" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An inhibition mechanism in which the effector binds a site distinct from the agonist's binding site (non-orthosteric), or irreversibly/insurmountably inactivates the receptor - reduces the receptor’s maximal response (Emax) in a way that cannot be overcome by adding more agonist." . a owl:Class ; rdfs:label "opening" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which an effector positively effects the normal functioning of an ion channel e.g., facilitates transport of ions through the channel." . a owl:Class ; rdfs:label "oxidation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A molecular modification mechanism in which an effector modifies a target substrate via an oxidation reaction." . a owl:Class ; rdfs:label "oxidoreduction" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which in which electrons are transferred between molecules catalyzed by an oxidoreductase enzyme." . a owl:Class ; rdfs:label "palmitoylation" ; @@ -3658,7 +3769,8 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "partial_agonism" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An agonism mechanism in which the effector binds to and only partially activates a receptor (relative to the response to a full agonist)" . a owl:Class ; rdfs:label "phosphorylation" ; @@ -3673,37 +3785,50 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "positive_allosteric_modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:broadMatch DGIdb:allosteric_modulator, + DGIdb:modulator ; + skos:closeMatch DGIdb:positive_allosteric_modulator, + CHEMBL.MECHANISM:positive_allosteric_modulator, + CHEMBL.MECHANISM:positive_modulator ; + skos:definition "A positive modulation mechanism in which the effector enhances the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)" . a owl:Class ; rdfs:label "post_transcriptional_regulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism which controls expression of a target gene at the RNA level after a gene has been transcribed into messenger RNA (mRNA)." . a owl:Class ; rdfs:label "potentiation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A positive modulation mechanism in which the effector binds to and enhances or intensifies the effect of some other chemical or drug on its target." . a owl:Class ; rdfs:label "reduction" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A molecular modification mechanism in which an effector modifies a target substrate via a reduction reaction." . a owl:Class ; rdfs:label "release" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch ; + skos:definition "A modulation mechanism in which an effector reverses the normal functioning of a transporter, causing release of the substrate, rather than uptake" . a owl:Class ; rdfs:label "relocalization" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism mediated by an effector that alters the localization of a target in the cell or body." . a owl:Class ; rdfs:label "rna_interference_inhibition" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A negative modulation mechanism in which an effector small interfering RNA (siRNA) molecule finds and destroys messenger RNA (mRNA) with a complementary sequence, preventing a specific gene from being translated into a protein. Note that while this is called \"inhibition', it is not inhibition in the classic biochemical sense that requires a direct interaction between effector and target." . a owl:Class ; rdfs:label "s_nitrosylation" ; @@ -3713,17 +3838,22 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "sequestration" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which an effector binds to a substance such as a drug, toxin or metabolite and reduces its availability for further interactions." . a owl:Class ; rdfs:label "signaling_mediated_control" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism mediated by the activation or control of signaling events that influence the some aspect of the target entity (e.g. its activity, processing, transport, etc.)." . a owl:Class ; rdfs:label "stimulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch SEMMEDDB:STIMULATES, + DGIdb:stimulator ; + skos:definition "An activation mechanism in which the effector directly or indirectly affects its target, stimulating a physiological response." . a owl:Class ; rdfs:label "sulfation" ; @@ -3738,22 +3868,26 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "suppression" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A negative modulation mechanism in which the effector directly or indirectly affects its target, suppressing a physiological process." . a owl:Class ; rdfs:label "transcriptional_regulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism mediated by through the control of target gene transcription." . a owl:Class ; rdfs:label "transglutamination" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A covalent binding mechanism involving formation of a covalent bond between a glutamine residue and an amine as catalyzed by a transglutaminase." . a owl:Class ; rdfs:label "translational_regulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism mediated by through the control of target gene translation." . a owl:Class ; rdfs:label "trimethylation" ; @@ -3768,11 +3902,13 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; a owl:Class ; rdfs:label "vaccine_antigen" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An immune system modulation mechanism in which a vaccine mediates its effect through the activation of the immune system against the target." . biolink:Cell a owl:Class ; rdfs:label "cell" ; rdfs:subClassOf biolink:AnatomicalEntity ; + skos:definition "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." ; skos:exactMatch MESH:D002477, STY:T025, , @@ -3784,21 +3920,22 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:CellLine ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + skos:definition "An association in which a cell line - typically derived from an organismal entity with a disease state - serves as a model for that disease in experimental settings." ; skos:inScheme biolink: . biolink:CellLineToEntityAssociationMixin a owl:Class ; @@ -3810,38 +3947,38 @@ biolink:CellLineToEntityAssociationMixin a owl:Class ; biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:integer ; owl:onProperty biolink:dgidb_evidence_score ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:supporting_documents ], + owl:onProperty biolink:evidence_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:dgidb_interaction_score ], + owl:onProperty biolink:dgidb_evidence_score ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:evidence_count ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; + owl:minCardinality 0 ; owl:onProperty biolink:dgidb_interaction_score ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:evidence_count ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:dgidb_evidence_score ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:supporting_documents ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:dgidb_interaction_score ], + owl:onProperty biolink:dgidb_evidence_score ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:integer ; owl:onProperty biolink:evidence_count ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:dgidb_interaction_score ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:dgidb_interaction_score ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:dgidb_evidence_score ], + owl:onProperty biolink:supporting_documents ], biolink:ChemicalAffectsBiologicalEntityAssociation ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; skos:inScheme biolink: . @@ -3849,31 +3986,31 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme biolink: . @@ -3881,41 +4018,41 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A regulatory relationship between two genes" ; skos:inScheme biolink: . @@ -3923,65 +4060,65 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; biolink:ChemicalEntityToBiologicalProcessAssociation a owl:Class ; rdfs:label "chemical entity to biological process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a chemical entity and a biological process, where the chemical entity has some effect on the biological process." ; skos:inScheme biolink: . @@ -3989,7 +4126,10 @@ biolink:ChemicalEntityToBiologicalProcessAssociation a owl:Class ; biolink:ChemicalEntityToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical entity to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:MacromolecularMachineMixin ; @@ -3998,28 +4138,25 @@ biolink:ChemicalEntityToChemicalDerivationAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:catalyst_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:ChemicalEntityToChemicalEntityAssociation ; skos:definition "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; @@ -4028,35 +4165,35 @@ biolink:ChemicalEntityToChemicalDerivationAssociation a owl:Class ; biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical entity to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:clinical_approval_status ], + owl:maxCardinality 1 ; + owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:allValuesFrom biolink:ResearchPhaseEnum ; + owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:max_research_phase ], + owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:max_research_phase ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ResearchPhaseEnum ; - owl:onProperty biolink:max_research_phase ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:max_research_phase ], biolink:Association ; skos:definition "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; skos:inScheme biolink: ; @@ -4065,22 +4202,22 @@ biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalEntityToPathwayAssociation a owl:Class ; rdfs:label "chemical entity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Pathway ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An interaction between a chemical entity and a biological process or pathway." ; @@ -4090,161 +4227,161 @@ biolink:ChemicalEntityToPathwayAssociation a owl:Class ; biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:dgidb_evidence_score ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:dgidb_evidence_score ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:dgidb_interaction_score ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:dgidb_interaction_score ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:dgidb_evidence_score ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AffinityMeasurement ; - owl:onProperty biolink:has_affinity ], + owl:minCardinality 0 ; + owl:onProperty biolink:dgidb_interaction_score ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:dgidb_evidence_score ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:dgidb_evidence_score ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:dgidb_interaction_score ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_affinity ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:dgidb_evidence_score ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom biolink:AffinityMeasurement ; + owl:onProperty biolink:has_affinity ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_affinity ], biolink:Association ; skos:broadMatch SIO:001257 ; skos:definition "describes an interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; @@ -4253,29 +4390,29 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; biolink:ChemicalOrDrugOrTreatmentAdverseEventAssociation a owl:Class ; rdfs:label "chemical or drug or treatment adverse event association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; - owl:onProperty biolink:FDA_adverse_event_level ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:FDA_adverse_event_level ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:FDA_adverse_event_level ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:FDA_adverse_event_level ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; + owl:onProperty biolink:FDA_adverse_event_level ], biolink:Association ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an untoward medical occurrence that happens during treatment, whether or not considered related to the treatment." ; skos:inScheme biolink: . @@ -4289,10 +4426,10 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -4304,6 +4441,9 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation a owl:Class ; biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; @@ -4312,9 +4452,6 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:C [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -4396,10 +4533,10 @@ biolink:ClinicalMeasurement a owl:Class ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], biolink:ClinicalAttribute ; skos:definition "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; @@ -4424,67 +4561,80 @@ biolink:ClinicalMeasurement a owl:Class ; a owl:Class ; rdfs:label "ACTIVE_NOT_RECRUITING" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The study is ongoing but not currently recruiting participants." . a owl:Class ; rdfs:label "APPROVED_FOR_MARKETING" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The intervention has received regulatory approval for marketing." . a owl:Class ; rdfs:label "AVAILABLE" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The intervention or data is available for use or distribution." . a owl:Class ; rdfs:label "COMPLETED" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The study has ended normally and participants are no longer being examined or treated." . a owl:Class ; rdfs:label "ENROLLING_BY_INVITATION" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Participants are being enrolled by invitation only." . a owl:Class ; rdfs:label "NOT_YET_RECRUITING" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The study has not yet started recruiting participants." . a owl:Class ; rdfs:label "NO_LONGER_AVAILABLE" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The intervention or data is no longer available." . a owl:Class ; rdfs:label "RECRUITING" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The study is currently recruiting participants." . a owl:Class ; rdfs:label "SUSPENDED" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The study has been temporarily halted but may resume." . a owl:Class ; rdfs:label "TEMPORARILY_NOT_AVAILABLE" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The intervention or data is not currently available but may become available later." . a owl:Class ; rdfs:label "TERMINATED" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The study has stopped prematurely and will not start again." . a owl:Class ; rdfs:label "UNKNOWN" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The recruitment or availability status is unknown." . a owl:Class ; rdfs:label "WITHDRAWN" ; rdfs:subClassOf biolink:ClinicalTrialStatusEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The study was halted before enrolling its first participant." . biolink:Cohort a owl:Class ; rdfs:label "cohort" ; @@ -4510,7 +4660,7 @@ biolink:CommonDataElement a owl:Class ; biolink:ComplexChemicalExposure a owl:Class ; rdfs:label "complex chemical exposure" ; rdfs:subClassOf biolink:ExposureEvent ; - skos:definition "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; + skos:definition "A complex chemical exposure is an intake of a chemical mixture, other than a drug." ; skos:inScheme biolink: . biolink:ComplexMolecularMixture a owl:Class ; @@ -4537,38 +4687,38 @@ biolink:ConfidenceLevel a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationContentEntity ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:InformationContentEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:qualifiers ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; skos:inScheme biolink: . @@ -4576,164 +4726,174 @@ biolink:ContributorAssociation a owl:Class ; biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ; rdfs:label "correlated gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:z_score ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:diseases_confidence_score ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:diseases_confidence_score ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; owl:onProperty biolink:diseases_confidence_score ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:z_score ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:allelic_requirement ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; owl:onProperty biolink:diseases_confidence_score ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; + owl:maxCardinality 1 ; owl:onProperty biolink:z_score ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:z_score ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:allelic_requirement ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( xsd:string [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^HP:\\d{7}$" ] ) ] ) ] ; owl:onProperty biolink:allelic_requirement ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( xsd:string [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^HP:\\d{7}$" ] ) ] ) ] ; + owl:maxCardinality 1 ; owl:onProperty biolink:allelic_requirement ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; + skos:definition "An association between a gene (or gene product) and a disease for which the gene is statistically correlated with the disease rather than asserted as causal. Such associations typically derive from GWAS, co-occurrence analyses, or other statistical methods, and are annotated with scores such as a z-score or a diseases confidence score." ; skos:inScheme biolink: . a owl:Class ; rdfs:label "downregulated" ; rdfs:subClassOf biolink:DirectionQualifierEnum, - . + ; + skos:broadMatch RO:0004033 ; + skos:closeMatch RO:0002335 ; + skos:exactMatch RO:0002212, + RO:0004035 . a owl:Class ; rdfs:label "upregulated" ; rdfs:subClassOf biolink:DirectionQualifierEnum, - . + ; + skos:closeMatch RO:0002336 ; + skos:exactMatch RO:0002213 ; + skos:narrowMatch RO:0002629, + RO:0004032, + RO:0004034 . biolink:DiseaseAssociatedWithResponseToChemicalEntityAssociation a owl:Class ; rdfs:label "disease associated with response to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:response_target_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ResponseEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:response_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:response_target_context_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ResponseTargetEnum ; - owl:onProperty biolink:response_target_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:response_target_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:response_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:response_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ResponseTargetEnum ; owl:onProperty biolink:response_target_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ResponseEnum ; + owl:onProperty biolink:response_context_qualifier ], biolink:Association ; skos:definition "A statistical association between a disease and a chemical entity where the chemical entity has a therapeutic or adverse effect on the disease progression, symptoms or outcomes in a patient, cell line, or any model system." ; skos:inScheme biolink: . @@ -4744,28 +4904,28 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PathologicalEntityMixin ], biolink:ExposureEvent ; - skos:definition "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; + skos:definition "A disease or phenotypic feature state, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome,." ; skos:inScheme biolink: . biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneticInheritance ; @@ -4777,17 +4937,17 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to location association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; skos:inScheme biolink: . @@ -4807,40 +4967,40 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:PhenotypicFeature ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FrequencyQuantifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Onset ; owl:onProperty biolink:onset_qualifier ], biolink:Association ; skos:closeMatch dcid:DiseaseSymptomAssociation ; @@ -4850,12 +5010,14 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; a owl:Class ; rdfs:label "over_the_counter" ; rdfs:subClassOf biolink:DrugAvailabilityEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "chemical entity is available over the counter without a prescription." . a owl:Class ; rdfs:label "prescription" ; rdfs:subClassOf biolink:DrugAvailabilityEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "chemical entity is available by prescription." . a owl:Class ; rdfs:label "absorption_through_the_skin" ; @@ -4903,16 +5065,16 @@ biolink:DrugToEntityAssociationMixin a owl:Class ; biolink:DrugToGeneAssociation a owl:Class ; rdfs:label "drug to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DrugToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a drug and a gene or gene product." ; @@ -4931,97 +5093,103 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; a owl:Class ; rdfs:label "tbio" ; rdfs:subClassOf biolink:DruggableGeneCategoryEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy the activity thresholds detailed below." . a owl:Class ; rdfs:label "tchem" ; rdfs:subClassOf biolink:DruggableGeneCategoryEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "These targets do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy one or more of the following criteria: target is above the cutoff criteria for the target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s) with an Experimental Evidence code" . a owl:Class ; rdfs:label "tclin" ; rdfs:subClassOf biolink:DruggableGeneCategoryEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action." . a owl:Class ; rdfs:label "tdark" ; rdfs:subClassOf biolink:DruggableGeneCategoryEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "These are targets about which virtually nothing is known. They do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy two or more of the following criteria: A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or less than or equal to 50 Antibodies available according to http://antibodypedia.com." . biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:druggable_gene_category ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; - owl:onProperty biolink:druggable_gene_category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:druggable_gene_category ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - biolink:GeneToDiseaseAssociation ; - skos:inScheme biolink: . - + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; + owl:onProperty biolink:druggable_gene_category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:druggable_gene_category ], + biolink:GeneToDiseaseAssociation ; + skos:definition "An association between a gene (or gene product) and a disease in which the gene is classified by its druggability (e.g., via the IDG/Pharos target development-level tiers)." ; + skos:inScheme biolink: . + biolink:EntityToDiseaseAssociation a owl:Class ; rdfs:label "entity to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:number_of_cases ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ResearchPhaseEnum ; - owl:onProperty biolink:max_research_phase ], + owl:minCardinality 0 ; + owl:onProperty biolink:FDA_regulatory_approvals ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:FDA_regulatory_approvals ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:number_of_cases ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_approval_status ], + owl:onProperty biolink:number_of_cases ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_approval_status ], + owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ResearchPhaseEnum ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:number_of_cases ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:minCardinality 0 ; + owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:FDA_regulatory_approvals ], + owl:onProperty biolink:clinical_approval_status ], biolink:Association ; + skos:definition "An association between any entity and a disease, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases." ; skos:inScheme biolink: . biolink:EntityToExposureEventAssociationMixin a owl:Class ; @@ -5039,50 +5207,54 @@ biolink:EntityToOutcomeAssociationMixin a owl:Class ; biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "entity to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_approval_status ], + owl:minCardinality 0 ; + owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:FDA_regulatory_approvals ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; - owl:onProperty biolink:clinical_approval_status ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ResearchPhaseEnum ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:number_of_cases ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:FDA_regulatory_approvals ], + owl:maxCardinality 1 ; + owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:number_of_cases ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:clinical_approval_status ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:number_of_cases ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:FDA_regulatory_approvals ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:number_of_cases ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ResearchPhaseEnum ; - owl:onProperty biolink:max_research_phase ], + owl:onProperty biolink:clinical_approval_status ], biolink:Association ; + skos:definition "An association between any entity and a phenotypic feature, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases." ; skos:inScheme biolink: . biolink:EnvironmentalFeature a owl:Class ; rdfs:label "environmental feature" ; rdfs:subClassOf biolink:PlanetaryEntity ; + skos:definition "A system or entity in the natural environment that has the disposition to environ one or more material entities." ; skos:exactMatch ; skos:inScheme biolink: . biolink:EnvironmentalFoodContaminant a owl:Class ; rdfs:label "environmental food contaminant" ; rdfs:subClassOf biolink:ChemicalEntity ; + skos:definition "Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate foodstuffs during their production, transportation or storage." ; + skos:exactMatch ; skos:inScheme biolink: ; skos:relatedMatch . @@ -5092,12 +5264,14 @@ biolink:EnvironmentalProcess a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:Occurrent ], biolink:PlanetaryEntity ; + skos:definition "A process that occurs within or involves the components of an environmental system." ; skos:exactMatch ; skos:inScheme biolink: . biolink:EpigenomicEntity a owl:Class ; rdfs:label "epigenomic entity" ; rdfs:subClassOf ; + skos:definition "A mixin for entities that represent epigenomic modifications or features associated with heritable changes in gene expression that do not involve changes to the DNA sequence itself." ; skos:inScheme biolink: . biolink:Event a owl:Class ; @@ -5117,6 +5291,12 @@ biolink:Evidence a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:object ], [ a owl:Restriction ; @@ -5125,15 +5305,9 @@ biolink:ExonToTranscriptRelationship a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" ; skos:inScheme biolink: . @@ -5148,19 +5322,19 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:temporal_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:temporal_context_qualifier ], + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:temporal_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], biolink:Association ; skos:definition "An association between an exposure event and an outcome." ; skos:inScheme biolink: . @@ -5170,15 +5344,15 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:ExposureEvent ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; skos:inScheme biolink: . @@ -5186,22 +5360,26 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; a owl:Class ; rdfs:label "life_threatening_adverse_event" ; rdfs:subClassOf biolink:FDAIDAAdverseEventEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. It does not include an adverse event or suspected adverse reaction that, had it occurred in a more severe form, might have caused death." . a owl:Class ; rdfs:label "serious_adverse_event" ; rdfs:subClassOf biolink:FDAIDAAdverseEventEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event, inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth defect. Important medical events that may not result in death, be life-threatening, or require hospitalization may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or subject and may require medical or surgical intervention to prevent one of the outcomes listed in this definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient hospitalization, or the development of drug dependency or drug abuse." . a owl:Class ; rdfs:label "suspected_adverse_reaction" ; rdfs:subClassOf biolink:FDAIDAAdverseEventEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug." . a owl:Class ; rdfs:label "unexpected_adverse_event" ; rdfs:subClassOf biolink:FDAIDAAdverseEventEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the investigator brochure or is not listed at the specificity or severity that has been observed; or, if an investigator brochure is not required or available, is not consistent with the risk information described in the general investigational plan or elsewhere in the current application, as amended. For example, under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but are not specifically mentioned as occurring with the particular drug under investigation." . biolink:FeatureOrDiseaseQualifiersToEntityMixin a owl:Class ; rdfs:label "feature or disease qualifiers to entity mixin" ; @@ -5212,19 +5390,22 @@ biolink:FeatureOrDiseaseQualifiersToEntityMixin a owl:Class ; biolink:Food a owl:Class ; rdfs:label "food" ; rdfs:subClassOf biolink:ChemicalMixture ; - skos:definition "A substance consumed by a living organism as a source of nutrition" ; + skos:definition "A substance of plant, animal, or artificial origin consumed by a living organism to provide essential nutrients, energy, and support growth and the processes of life, or to satisfy other health needs or provide a social or organoleptic experience." ; + skos:exactMatch , + ; skos:inScheme biolink: . biolink:FoodAdditive a owl:Class ; rdfs:label "food additive" ; rdfs:subClassOf biolink:ChemicalEntity ; + skos:definition "Any substance which is added to food to preserve or enhance its flavour and/or appearance." ; + skos:exactMatch ; skos:inScheme biolink: ; skos:relatedMatch . biolink:Fungus a owl:Class ; rdfs:label "fungus" ; rdfs:subClassOf biolink:CellularOrganism ; - skos:definition "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; skos:exactMatch STY:T004, , ; @@ -5235,173 +5416,173 @@ biolink:Fungus a owl:Class ; biolink:GeneAffectsChemicalAssociation a owl:Class ; rdfs:label "gene affects chemical association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; skos:inScheme biolink: . @@ -5412,48 +5593,49 @@ biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:GeneToDiseaseAssociation ; + skos:definition "An association in which a gene (e.g., a model-organism ortholog of a known disease gene) serves as a model of a human disease - for example, because mutants of the gene recapitulate core features of the disease." ; skos:inScheme biolink: . biolink:GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation a owl:Class ; rdfs:label "gene family to gene or gene product or gene family association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneFamily ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Relationship between a gene family and a contained gene or gene product or gene family." ; @@ -5465,7 +5647,7 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -5474,30 +5656,31 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:GeneToDiseaseAssociation ; + skos:definition "A gene-to-disease association that is asserted on the grounds that the gene harbours a sequence variant that contributes to the disease. Qualifies the gene with the form or variant that underlies the contribution." ; skos:inScheme biolink: . a owl:Class ; @@ -5793,22 +5976,22 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation a owl:Class ; rdfs:label "gene or gene product or gene family to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrGeneFamily ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProductOrGeneFamily ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a gene or gene product or gene family and an anatomical entity." ; @@ -5817,31 +6000,31 @@ biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation a owl:Class ; biolink:GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation a owl:Class ; rdfs:label "gene or gene product or gene family to biological process or activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcessOrActivity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrGeneFamily ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProductOrGeneFamily ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Relationship between a gene or gene product or gene family to a specified biological process or activity (e.g. molecular activity, biological process or pathway)." ; @@ -5851,77 +6034,77 @@ biolink:GeneRegulatesGeneAssociation a owl:Class ; rdfs:label "gene regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme biolink: . - a owl:Class ; + a owl:Class ; rdfs:label "biolink:associated_with" ; rdfs:subClassOf biolink:GeneToDiseasePredicateEnum, linkml:PermissibleValue . - a owl:Class ; + a owl:Class ; rdfs:label "biolink:contributes_to" ; rdfs:subClassOf biolink:GeneToDiseasePredicateEnum, linkml:PermissibleValue . @@ -5930,59 +6113,59 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:label "gene to expression site association" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:object_specialization_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_specialization_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:maxCardinality 1 ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:object_specialization_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onProperty biolink:object_specialization_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_specialization_qualifier ], + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" ; @@ -5991,17 +6174,17 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneExpressionMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; skos:inScheme biolink: . @@ -6013,25 +6196,25 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneFamily ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneFamily ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -6043,64 +6226,64 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - biolink:GeneToGeneAssociation ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + biolink:GeneToGeneAssociation ; skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; skos:inScheme biolink: . biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneProductMixin ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneProductMixin ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" ; skos:inScheme biolink: . @@ -6109,16 +6292,16 @@ biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -6127,6 +6310,7 @@ biolink:GeneToGoTermAssociation a owl:Class ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; + skos:definition "A functional association between a gene (or gene product or macromolecular complex) and a Gene Ontology (GO) term describing the molecular function, biological process, or cellular component in which it participates." ; skos:exactMatch WBVocab:Gene-GO-Association ; skos:inScheme biolink: . @@ -6134,13 +6318,10 @@ biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -6148,10 +6329,13 @@ biolink:GeneToPathwayAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." ; @@ -6160,44 +6344,35 @@ biolink:GeneToPathwayAssociation a owl:Class ; biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:allelic_requirement ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneToPhenotypicFeaturePredicateEnum ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:allValuesFrom biolink:GeneToPhenotypicFeaturePredicateEnum ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:allelic_requirement ], @@ -6205,33 +6380,43 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:allelic_requirement ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( xsd:string [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^HP:\\d{7}$" ] ) ] ) ] ; owl:onProperty biolink:allelic_requirement ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], biolink:Association ; + skos:definition "An association between a gene or gene product and a phenotypic feature, where variation in the gene is correlated with the phenotypic feature." ; skos:exactMatch WBVocab:Gene-Phenotype-Association ; skos:inScheme biolink: ; skos:narrowMatch SIO:000983, @@ -6240,22 +6425,22 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; "for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype", "if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children." . - a owl:Class ; + a owl:Class ; rdfs:label "biolink:associated_with" ; rdfs:subClassOf biolink:GeneToPhenotypicFeaturePredicateEnum, linkml:PermissibleValue . - a owl:Class ; + a owl:Class ; rdfs:label "biolink:causes" ; rdfs:subClassOf biolink:GeneToPhenotypicFeaturePredicateEnum, linkml:PermissibleValue . - a owl:Class ; + a owl:Class ; rdfs:label "biolink:contributes_to" ; rdfs:subClassOf biolink:GeneToPhenotypicFeaturePredicateEnum, linkml:PermissibleValue . - a owl:Class ; + a owl:Class ; rdfs:label "biolink:has_phenotype" ; rdfs:subClassOf biolink:GeneToPhenotypicFeaturePredicateEnum, linkml:PermissibleValue . @@ -6267,10 +6452,10 @@ biolink:Genome a owl:Class ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:closeMatch dcid:GenomeAssemblyUnit ; skos:definition "A genome is the sum of genetic material within a cell or virion." ; @@ -6283,19 +6468,19 @@ biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], + owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], biolink:ExposureEvent ; skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; skos:inScheme biolink: . @@ -6303,12 +6488,6 @@ biolink:GenomicBackgroundExposure a owl:Class ; biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "genotype as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; @@ -6317,26 +6496,30 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], biolink:GenotypeToDiseaseAssociation ; + skos:definition "An association in which a genotype serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it." ; skos:inScheme biolink: . biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -6344,8 +6527,11 @@ biolink:GenotypeToGeneAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -6356,32 +6542,32 @@ biolink:GenotypeToGeneAssociation a owl:Class ; biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" ; skos:inScheme biolink: . @@ -6389,14 +6575,11 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -6404,14 +6587,17 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; skos:inScheme biolink: . @@ -6419,32 +6605,32 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." ; skos:inScheme biolink: . @@ -6480,13 +6666,13 @@ biolink:GeographicExposure a owl:Class ; biolink:GeographicLocationAtTime a owl:Class ; rdfs:label "geographic location at time" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:timepoint ], biolink:GeographicLocation ; skos:definition "a location that can be described in lat/long coordinates, for a particular time" ; @@ -6497,6 +6683,7 @@ biolink:GrossAnatomicalStructure a owl:Class ; rdfs:subClassOf biolink:AnatomicalEntity ; skos:altLabel "organ", "tissue" ; + skos:definition "An anatomical structure that has more than one cell as a part." ; skos:exactMatch , WIKIDATA:Q4936952 ; skos:inScheme biolink: ; @@ -6507,14 +6694,14 @@ biolink:GrossAnatomicalStructure a owl:Class ; biolink:Haplotype a owl:Class ; rdfs:label "haplotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:definition "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; skos:exactMatch , @@ -6525,6 +6712,7 @@ biolink:Haplotype a owl:Class ; biolink:Hospitalization a owl:Class ; rdfs:label "hospitalization" ; rdfs:subClassOf biolink:ClinicalIntervention ; + skos:definition "The admission and care of a patient in a hospital for observation, diagnosis, or treatment." ; skos:exactMatch SNOMEDCT:32485007, WIKIDATA:Q3140971 ; skos:inScheme biolink: . @@ -6535,7 +6723,6 @@ biolink:Human a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:SubjectOfInvestigation ], biolink:Mammal ; - skos:definition "A member of the the species Homo sapiens." ; skos:exactMatch STY:T016, , , @@ -6545,74 +6732,74 @@ biolink:Human a owl:Class ; biolink:IceesStudyResult a owl:Class ; rdfs:label "icees study result" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:log_odds_ratio_95_ci ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:chi_squared_p ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:chi_squared_p ], + owl:maxCardinality 1 ; + owl:onProperty biolink:chi_squared_statistic ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:fisher_exact_p ], [ a owl:Restriction ; owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:chi_squared_dof ], + owl:onProperty biolink:total_sample_size ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:fisher_exact_odds_ratio ], + owl:onProperty biolink:total_sample_size ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:chi_squared_statistic ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:fisher_exact_odds_ratio ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:fisher_exact_p ], + owl:onProperty biolink:log_odds_ratio ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; - owl:onProperty biolink:chi_squared_statistic ], + owl:onProperty biolink:log_odds_ratio ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:log_odds_ratio_95_ci ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:log_odds_ratio ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:chi_squared_statistic ], + owl:onProperty biolink:chi_squared_p ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:total_sample_size ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:chi_squared_dof ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; - owl:onProperty biolink:fisher_exact_odds_ratio ], + owl:onProperty biolink:chi_squared_p ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; - owl:onProperty biolink:chi_squared_p ], + owl:onProperty biolink:chi_squared_statistic ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:log_odds_ratio ], + owl:onProperty biolink:chi_squared_dof ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; - owl:onProperty biolink:log_odds_ratio ], + owl:onProperty biolink:fisher_exact_odds_ratio ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:chi_squared_dof ], + owl:onProperty biolink:fisher_exact_p ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:fisher_exact_odds_ratio ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:total_sample_size ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; - owl:onProperty biolink:fisher_exact_p ], + owl:onProperty biolink:log_odds_ratio_95_ci ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:chi_squared_dof ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:log_odds_ratio ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:fisher_exact_p ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:total_sample_size ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:total_sample_size ], + owl:minCardinality 0 ; + owl:onProperty biolink:fisher_exact_odds_ratio ], biolink:StudyResult ; skos:definition "A study result that represents a result, from a supporting Study, which is specifically associated with an Integrated Clinical and Environmental Exposures Service (ICEES) knowledge assertion." ; skos:inScheme biolink: . @@ -6620,14 +6807,11 @@ biolink:IceesStudyResult a owl:Class ; biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:label "information content entity to named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -6635,17 +6819,20 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; skos:inScheme biolink: . @@ -6653,7 +6840,6 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; biolink:Invertebrate a owl:Class ; rdfs:label "invertebrate" ; rdfs:subClassOf biolink:CellularOrganism ; - skos:definition "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; skos:exactMatch STY:T011, , , @@ -6672,37 +6858,54 @@ biolink:JournalArticle a owl:Class ; a owl:Class ; rdfs:label "knowledge_assertion" ; rdfs:subClassOf biolink:KnowledgeLevelEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:altLabel "assertion" ; + skos:definition "A statement of purported fact that is put forth by an agent as true, based on assessment of direct evidence. Assertions are likely but not definitively true." ; + skos:editorialNote "Knowledge Assertions are supported by direct evidence deemed sufficient by some agent to support a confidence assertion of truth. Our certainty in this truth is not absolute, but is typically higher than for Predictions." . a owl:Class ; rdfs:label "logical_entailment" ; rdfs:subClassOf biolink:KnowledgeLevelEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:altLabel "deductive_inference" ; + skos:definition "A statement reporting a conclusion that follows logically from premises representing established facts or knowledge assertions (e.g. fingernail part of finger, finger part of hand --> fingernail part of hand)." ; + skos:editorialNote "These statements report entailed conclusions derived through dedictive inference. They are not directly asserted by a source, but logically follow from statement(s) a source does make - and are necessarily true if their supporting premises are true. In practice, these will primarily be entailments based on logic encoded in ontologies. Examples include propagation of annotated knowledge to hierarchically-related concepts, across paths through a graph constructed from transitive relationships, or sets of relationships that support property chain inference." . a owl:Class ; rdfs:label "not_provided" ; rdfs:subClassOf biolink:KnowledgeLevelEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "The knowledge level is not provided, typically because it cannot be determined from available. information." ; + skos:editorialNote "This term is most often applied for text-mined edges, as NLP tools are typically not able to detect a specific knowledge level for the concept relationships they extract (e.g. whether the author was predicting or asserting a relationship, or merely observed it to occur)." . a owl:Class ; rdfs:label "observation" ; rdfs:subClassOf biolink:KnowledgeLevelEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A statement reporting (and possibly quantifying) a phenomenon that was observed to occur - absent any analysis or interpretation that generates a statistical association or supports a broader conclusion or inference." ; + skos:editorialNote "An observation that \"56362 people self-reported taking melatonin to treat migraines\" is agnostic to whether melatonin is an effective or approved treatment - it only claims that it was taken for this purpose. Such observations, however, may be used as the basis for predicting that a drug may be efficacious against a disease." . a owl:Class ; rdfs:label "prediction" ; rdfs:subClassOf biolink:KnowledgeLevelEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:altLabel "hypothesis" ; + skos:definition "A statement of a possible fact based on probabilistic forms of reasoning over more indirect forms of evidence, that lead to more speculative conclusions." ; + skos:editorialNote "Predictions typically result from non-deductive forms of reasoning - e.g. inductive and deductive inference, or statistical inference where conclusions are drawn about a broader/global population based on data from a representative cohort. For example, a prediction that a drug may treat a particular disease based on its chemical similarity to known drugs that treat the disease, and the fact that it can inhibit proteins in a pathway that is associated with the disease As Predictions are based on weaker forms of inference and evidence, they are typically considered lower confidence statements as compared to Knowledge Assertions and Logical Entailments." . a owl:Class ; rdfs:label "statistical_association" ; rdfs:subClassOf biolink:KnowledgeLevelEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A statement that reports concepts representing variables in a dataset to be statistically associated with each other in a particular cohort (e.g. 'Metformin Treatment (variable 1) is correlated with Diabetes Diagnosis (variable 2) in EHR dataset X')." ; + skos:editorialNote "Such statements report the direct results of some statistical analysis. Their scope is limited tp the cohort/dataset interrogated in the analysis, and they do not make broader claims or draw more meaningful conclusions about the domain of discourse. Note however that such Statistical Associations can be used as evidence to support a more pointed/precise Prediction or Assertion of knowledge. For example, e.g. a Statistical Association between 'Metformin Prescription' and 'Diabetes Diagnosis' in EHR records could support a Prediction that 'Metformin treats Diabetes', or 'Metformin causes Diabetes'. This 'treats' edge may have a knowledge_level of 'Prediction', but the provider could use the 'evidence_type' edge property to indicate that this prediction is based on a 'Statistical Association'. Because Statistical Associations directly report analysis-specific results, we can consider them to be inherently true statements, whose broader utility is dependent on subsequent generalization of the reported result to a broader population, and/or interpretation of the result as support for a more meaningful statements about the domain of discourse." . a owl:Class ; rdfs:label "text_co_occurrence" ; rdfs:subClassOf biolink:KnowledgeLevelEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A statement reporting that mentions of two concepts in some corpus of text (e.g. the biomedical literature) occur together at a statistically significant frequency - suggesting that a real-world biological or clinical relationship may exist between the concepts." ; + skos:editorialNote "Such statements often utilize NLP/text-mining to identify concept mentions in text, but the reported statement is generated by a data analysis pipeline that performs calculations on mention counts and determines the strength of their correlation." . biolink:LogOddsAnalysisResult a owl:Class ; rdfs:label "log odds analysis result" ; @@ -6729,31 +6932,31 @@ biolink:MacromolecularComplex a owl:Class ; biolink:MacromolecularMachineHasSubstrateAssociation a owl:Class ; rdfs:label "macromolecular machine has substrate association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Describes the relationship between an enzyme (usually a macromolecular complex or gene product) and the molecules it acts on (substrate). The substrate can be a chemical, a polypeptide, or a protein." ; @@ -6765,15 +6968,15 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; skos:inScheme biolink: . @@ -6781,17 +6984,17 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; rdfs:label "macromolecular machine to cellular component association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:CellularComponent ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; skos:inScheme biolink: . @@ -6801,15 +7004,15 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; skos:inScheme biolink: . @@ -6818,19 +7021,19 @@ biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:MaterialSample ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:predicate ], @@ -6841,8 +7044,8 @@ biolink:MaterialSampleDerivationAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." ; skos:inScheme biolink: . @@ -6868,6 +7071,7 @@ biolink:MaterialSampleToEntityAssociationMixin a owl:Class ; biolink:MicroRNA a owl:Class ; rdfs:label "microRNA" ; rdfs:subClassOf biolink:NoncodingRNAProduct ; + skos:definition "A small (~22 nucleotide) RNA molecule that is the endogenous transcript of a miRNA gene. Produced from precursor molecules that form hairpin structures, which are processed (typically via the Dicer pathway) to yield a single miRNA molecule. miRNAs function by triggering cleavage of target molecules or acting as translational repressors." ; skos:exactMatch , SIO:001397, WIKIDATA:Q310899 ; @@ -6876,16 +7080,13 @@ biolink:MicroRNA a owl:Class ; biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; @@ -6893,6 +7094,9 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; skos:inScheme biolink: . @@ -6901,22 +7105,22 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; skos:inScheme biolink: . @@ -6924,32 +7128,32 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:MolecularActivity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Pathway ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; skos:inScheme biolink: . @@ -6957,100 +7161,101 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:population_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], biolink:Association ; + skos:definition "An association in which the subject entity is linked to the likelihood of the object entity occurring, manifesting, or being observed. Subject and object may each be qualified by aspect and context, and the association may be further qualified by a population context." ; skos:inScheme biolink: . biolink:NucleicAcidSequenceMotif a owl:Class ; rdfs:label "nucleic acid sequence motif" ; rdfs:subClassOf biolink:BiologicalEntity ; skos:altLabel "consensus sequence" ; - skos:definition "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; + skos:definition "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. consensus sequences." ; skos:inScheme biolink: . biolink:NucleosomeModification a owl:Class ; rdfs:label "nucleosome modification" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneProductIsoformMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EpigenomicEntity ], biolink:BiologicalEntity ; - skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; + skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform." ; skos:inScheme biolink: . biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ; @@ -7064,74 +7269,75 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; + skos:definition "An abstract association between an organism taxon and an environmental context (e.g., a habitat, biome, or ecological setting) in which the taxon occurs." ; skos:inScheme biolink: . biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:associated_environmental_context ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; skos:inScheme biolink: . @@ -7139,14 +7345,17 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], @@ -7155,16 +7364,13 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; skos:inScheme biolink: . @@ -7172,7 +7378,7 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:label "organism to organism association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:IndividualOrganism ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -7180,16 +7386,17 @@ biolink:OrganismToOrganismAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:IndividualOrganism ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; + skos:definition "An association between two individual organisms (e.g., symbiosis, parasitism, predation, or other inter-organism relationships)." ; skos:inScheme biolink: . biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; @@ -7197,9 +7404,6 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismalEntity ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -7209,7 +7413,11 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismalEntity ; + owl:onProperty biolink:subject ], biolink:Association ; + skos:definition "An association in which an organismal entity (e.g., a strain or breed) serves as a model of a disease, either because it has a natural predisposition to the disease or was bred or engineered specifically to recapitulate it." ; skos:inScheme biolink: . biolink:PairwiseMolecularInteraction a owl:Class ; @@ -7217,48 +7425,48 @@ biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:interacting_molecules_category ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:interacting_molecules_category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:interacting_molecules_category ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; skos:inScheme biolink: . @@ -7275,7 +7483,7 @@ biolink:Patent a owl:Class ; biolink:PathologicalAnatomicalExposure a owl:Class ; rdfs:label "pathological anatomical exposure" ; rdfs:subClassOf biolink:ExposureEvent ; - skos:definition "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; + skos:definition "An abnormal anatomical structure, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome." ; skos:inScheme biolink: . biolink:PathologicalAnatomicalStructure a owl:Class ; @@ -7307,7 +7515,7 @@ biolink:PathologicalProcess a owl:Class ; biolink:PathologicalProcessExposure a owl:Class ; rdfs:label "pathological process exposure" ; rdfs:subClassOf biolink:ExposureEvent ; - skos:definition "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; + skos:definition "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome." ; skos:inScheme biolink: . a owl:Class ; @@ -7344,21 +7552,22 @@ biolink:Phenomenon a owl:Class ; biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ; rdfs:label "phenotypic feature to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:Association ; + skos:definition "An association between a phenotypic feature (sign or symptom) and a disease, where the phenotypic feature is a manifestation or clinical indicator of the disease." ; skos:inScheme biolink: . biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a owl:Class ; @@ -7377,9 +7586,9 @@ biolink:PhenotypicQuality a owl:Class ; rdfs:label "phenotypic quality" ; rdfs:subClassOf biolink:OrganismAttribute ; skos:altLabel "phenotypic properties" ; - skos:definition "A property of a phenotype" ; - skos:inScheme biolink: ; - skos:mappingRelation . + skos:broadMatch ; + skos:definition "A characteristic of a phenotype (e.g., weight, size, shape, color) that can be observed, measured, or compared across organisms or conditions." ; + skos:inScheme biolink: . biolink:PhenotypicSex a owl:Class ; rdfs:label "phenotypic sex" ; @@ -7395,6 +7604,7 @@ biolink:PhysiologicalProcess a owl:Class ; owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalProcess ; skos:altLabel "physiology" ; + skos:definition "A biological or chemical function within a living organism." ; skos:exactMatch STY:T039, WIKIDATA:Q30892994 ; skos:inScheme biolink: ; @@ -7416,30 +7626,30 @@ biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a two populations" ; @@ -7451,197 +7661,198 @@ biolink:PosttranslationalModification a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneProductIsoformMixin ], biolink:BiologicalEntity ; - skos:definition "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; + skos:definition "A chemical modification of a polypeptide or protein that occurs after translation, altering its structure, activity, localization, or interactions." ; + skos:exactMatch ; skos:inScheme biolink: . biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:exact_match ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:broad_match ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:narrow_match ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:mapped_predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:broad_match ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 0 ; owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:exact_match ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:mapped_predicate ], + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], linkml:ClassDefinition ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; skos:inScheme biolink: . @@ -7657,32 +7868,32 @@ biolink:PreprintPublication a owl:Class ; biolink:ProcessRegulatesProcessAssociation a owl:Class ; rdfs:label "process regulates process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcess ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme biolink: . @@ -7703,7 +7914,7 @@ biolink:ProteinDomain a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; - skos:definition "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; + skos:definition "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found." ; skos:exactMatch , , SIO:001379 ; @@ -7718,6 +7929,7 @@ biolink:ProteinFamily a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; + skos:definition "A set of proteins coding for diverse functions which, by virtue of their high degree of sequence similarity, are believed to have evolved from a single ancestral gene." ; skos:exactMatch , WIKIDATA:Q2278983 ; skos:inScheme biolink: ; @@ -7732,8 +7944,9 @@ biolink:ProteinIsoform a owl:Class ; owl:someValuesFrom biolink:GeneProductIsoformMixin ], biolink:Protein ; skos:altLabel "proteoform" ; - skos:definition "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; - skos:inScheme biolink: . + skos:definition "Represents a protein that is a specific isoform of the canonical or reference protein." ; + skos:inScheme biolink: ; + skos:note "See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" . biolink:RNAProductIsoform a owl:Class ; rdfs:label "RNA product isoform" ; @@ -7777,15 +7990,16 @@ biolink:RNAProductIsoform a owl:Class ; biolink:ReactionToCatalystAssociation a owl:Class ; rdfs:label "reaction to catalyst association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], biolink:ReactionToParticipantAssociation ; + skos:definition "A specialization of reaction-to-participant association in which the participant is a gene or gene product (e.g., an enzyme) that catalyses the reaction." ; skos:inScheme biolink: . biolink:ReagentTargetedGene a owl:Class ; @@ -7795,10 +8009,10 @@ biolink:ReagentTargetedGene a owl:Class ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:altLabel "sequence targeting reagent" ; skos:definition "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; @@ -7814,32 +8028,40 @@ biolink:RelativeFrequencyAnalysisResult a owl:Class ; a owl:Class ; rdfs:label "clinical_trial_phase_1" ; rdfs:subClassOf biolink:ResearchPhaseEnum, - . + ; + skos:definition "In the FDA Clinical Trial Phase, the Clinical Trial Phase 1 involves 20 – 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase." . a owl:Class ; rdfs:label "clinical_trial_phase_1_to_2" ; + rdfs:seeAlso ; rdfs:subClassOf biolink:ResearchPhaseEnum, - . + ; + skos:definition "A study that tests the safety, side effects, and best dose of a new treatment. Phase I/II clinical trials also test how well a certain type of cancer or other disease responds to a new treatment. In the phase II part of the clinical trial, patients usually receive the highest dose of treatment that did not cause harmful side effects in the phase I part of the clinical trial. Combining phases I and II may allow research questions to be answered more quickly or with fewer patients. Also called phase 1/phase 2 clinical trial." . a owl:Class ; rdfs:label "clinical_trial_phase_2" ; rdfs:subClassOf biolink:ResearchPhaseEnum, - . + ; + skos:definition "In the FDA Clinical Trial Phase, the Clinical Trial Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur." . a owl:Class ; rdfs:label "clinical_trial_phase_2_to_3" ; + rdfs:seeAlso ; rdfs:subClassOf biolink:ResearchPhaseEnum, - . + ; + skos:definition "A study that tests how well a new treatment works for a certain type of cancer or other disease and compares the new treatment with a standard treatment. Phase II/III clinical trials may also provide more information about the safety and side effects of the new treatment. Combining phases II and III may allow research questions to be answered more quickly or with fewer patients. Also called phase 2/phase 3 clinical trial." . a owl:Class ; rdfs:label "clinical_trial_phase_3" ; rdfs:subClassOf biolink:ResearchPhaseEnum, - . + ; + skos:definition "In the FDA Clinical Trial Phase, the Clinical Trial Phase 3 involves 300 – 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions." . a owl:Class ; rdfs:label "clinical_trial_phase_4" ; rdfs:subClassOf biolink:ResearchPhaseEnum, - . + ; + skos:definition "In the FDA Clinical Trial Phase, the Clinical Trial Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review." . a owl:Class ; rdfs:label "not_provided" ; @@ -7849,7 +8071,9 @@ biolink:RelativeFrequencyAnalysisResult a owl:Class ; a owl:Class ; rdfs:label "pre_clinical_research_phase" ; rdfs:subClassOf biolink:ResearchPhaseEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Biolink 'pre_clinical_research' is the union of both the `FDA discovery and development phase` and `FDA preclinical research phase`. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo." ; + skos:editorialNote "DrugBank calls this 'experimental'." . a owl:Class ; rdfs:label "aggregator_knowledge_source" ; @@ -7869,68 +8093,79 @@ biolink:RelativeFrequencyAnalysisResult a owl:Class ; a owl:Class ; rdfs:label "negative" ; rdfs:subClassOf biolink:ResponseEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A negative response to a treatment or intervention" . a owl:Class ; rdfs:label "therapeutic_response" ; rdfs:subClassOf biolink:ResponseEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A positive response to a treatment or intervention" . - a owl:Class ; + a owl:Class ; rdfs:label "cell line" ; rdfs:subClassOf biolink:ResponseTargetEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A cell line that is the target of a treatment or intervention" . a owl:Class ; rdfs:label "cohort" ; rdfs:subClassOf biolink:ResponseTargetEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A group of individuals that are the target of a treatment or intervention" . a owl:Class ; rdfs:label "individual" ; rdfs:subClassOf biolink:ResponseTargetEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "An individual that is the target of a treatment or intervention" . a owl:Class ; rdfs:label "sample" ; rdfs:subClassOf biolink:ResponseTargetEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A biological materialsample that is the target of a treatment or intervention" . biolink:SequenceEnum a owl:Class ; + rdfs:label "SequenceEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "type of sequence" ; + skos:inScheme biolink: ; linkml:permissible_values , . a owl:Class ; rdfs:label "aa" ; rdfs:subClassOf biolink:SequenceEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "amino acid" . a owl:Class ; rdfs:label "na" ; rdfs:subClassOf biolink:SequenceEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "nucleic acid" . biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Treatment ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Treatment ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; @@ -7940,46 +8175,46 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:maxCardinality 1 ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], biolink:Publication ; skos:altLabel "journal" ; @@ -8035,33 +8270,38 @@ biolink:SocioeconomicExposure a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:has_attribute ], biolink:ExposureEvent ; - skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; + skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual." ; skos:inScheme biolink: . biolink:SpecificityQuantifier a owl:Class ; rdfs:label "specificity quantifier" ; rdfs:subClassOf biolink:RelationshipQuantifier ; + skos:definition "A relationship quantifier that measures the specificity of a relationship, such as the proportion of true negatives correctly identified in a diagnostic or association context." ; skos:inScheme biolink: . - a owl:Class ; + a owl:Class ; rdfs:label "+" ; rdfs:subClassOf biolink:StrandEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Positive" . + + a owl:Class ; + rdfs:label "?" ; + rdfs:subClassOf biolink:StrandEnum, + linkml:PermissibleValue ; + skos:definition "Unknown" . a owl:Class ; rdfs:label "-" ; rdfs:subClassOf biolink:StrandEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Negative" . a owl:Class ; rdfs:label "." ; rdfs:subClassOf biolink:StrandEnum, - linkml:PermissibleValue . - - a owl:Class ; - rdfs:label "?" ; - rdfs:subClassOf biolink:StrandEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Unstranded" . biolink:StudyVariable a owl:Class ; rdfs:label "study variable" ; @@ -8075,24 +8315,25 @@ biolink:StudyVariable a owl:Class ; biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; + skos:definition "An association between two organism taxa, capturing ecological or evolutionary relationships between the taxa (e.g., a host-pathogen relationship or shared habitat)." ; skos:inScheme biolink: . biolink:TaxonomicRank a owl:Class ; @@ -8105,29 +8346,32 @@ biolink:TaxonomicRank a owl:Class ; biolink:TextMiningStudyResult a owl:Class ; rdfs:label "text mining study result" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:supporting_text ], + owl:maxCardinality 1 ; + owl:onProperty biolink:supporting_text_section_type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:supporting_document_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:supporting_text_section_type ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:extraction_confidence_score ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_location_in_text ], + owl:onProperty biolink:supporting_text_section_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:supporting_document_year ], + owl:onProperty biolink:object_location_in_text ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:extraction_confidence_score ], + owl:onProperty biolink:supporting_document_year ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:supporting_document_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:supporting_text ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:object_location_in_text ], + owl:minCardinality 0 ; + owl:onProperty biolink:supporting_document_year ], [ a owl:Restriction ; owl:allValuesFrom xsd:integer ; owl:onProperty biolink:supporting_document_year ], @@ -8135,29 +8379,26 @@ biolink:TextMiningStudyResult a owl:Class ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:extraction_confidence_score ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:supporting_text ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:supporting_document_year ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:object_location_in_text ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:supporting_document_type ], + owl:onProperty biolink:extraction_confidence_score ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:subject_location_in_text ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:supporting_document_type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:supporting_text_section_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_location_in_text ], + owl:onProperty biolink:supporting_document_type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:subject_location_in_text ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:supporting_text ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:supporting_text_section_type ], + owl:onProperty biolink:subject_location_in_text ], biolink:StudyResult ; skos:definition "A study result that represents information extracted from text using natural language processing techniques. This includes the extracted text, location offsets within the source document, confidence scores, and other metadata related to the text mining process." ; skos:inScheme biolink: . @@ -8165,23 +8406,23 @@ biolink:TextMiningStudyResult a owl:Class ; biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is a collection of transcripts" ; skos:inScheme biolink: . @@ -8190,16 +8431,16 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; rdfs:label "transcription factor binding site" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:RegulatoryRegion ; skos:altLabel "binding site", "tf binding site" ; @@ -8210,31 +8451,32 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "variant as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:VariantToDiseaseAssociation ; + skos:definition "An association in which a sequence variant serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it." ; skos:inScheme biolink: . biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], @@ -8248,79 +8490,80 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; + skos:definition "An association between a sequence variant and a phenotypic feature, in which the allele state of the variant is linked to the manifestation of the phenotype." ; skos:inScheme biolink: . biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQualifierMixin ], biolink:Association ; skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" ; skos:inScheme biolink: . @@ -8328,7 +8571,6 @@ biolink:VariantToPopulationAssociation a owl:Class ; biolink:Vertebrate a owl:Class ; rdfs:label "vertebrate" ; rdfs:subClassOf biolink:CellularOrganism ; - skos:definition "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; skos:exactMatch STY:T010, , ; @@ -8344,7 +8586,8 @@ biolink:Virus a owl:Class ; skos:definition "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; skos:exactMatch STY:T005, ; - skos:inScheme biolink: . + skos:inScheme biolink: ; + skos:note "see: https://github.com/OBOFoundry/COB/pull/211" . biolink:WebPage a owl:Class ; rdfs:label "web page" ; @@ -8386,8 +8629,9 @@ biolink:aggregator_knowledge_source a owl:DatatypeProperty ; skos:editorialNote "For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, the Edge is passed to the Ranking Agent’s ARAGORN ARA, and then on to the ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of data from which the knowledge was derived. The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP- generated knowledge is \"infores:unc-cdw-health.\" The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"" ; skos:inScheme biolink: . -biolink:aspect_qualifier a owl:DatatypeProperty ; +biolink:aspect_qualifier a owl:ObjectProperty ; rdfs:label "aspect qualifier" ; + rdfs:range biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; rdfs:subPropertyOf biolink:qualifier ; skos:definition "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association." ; skos:editorialNote "for good examples of aspects in the gene-> chemical space, please see the GeneOrGeneProductOrChemicalEntityAspectEnum (below) which lists many aspects that can be used to qualify the gene making the full subject a different ontological type. the qualifier ‘expression’ combines with a core concept of ‘Gene X’ to express the composed concept ‘expression of Gene X’ (Gene → Biological Process) the qualifier ‘exposure’ combines with a core concept of ‘Chemical X’ to express the composed concept ‘exposure to Chemical X’ (Chemical → Exposure Process) the qualifier ‘activity’ combines with a core concept of ‘PPARG’ to express the concept ‘activity of PPARG’ (Gene → function/activity) the qualifier ‘emergency Department Visit’ combines with a core concept of ‘Disease X’ to express the concept ‘Emergency Department visits for Disease X’ (Disease → Clinical Event) the qualifier ‘infection’ combines with a core concept of ‘Giardia’ to express the concept ‘Infection with Giardia’ (Taxon → Biological / Pathological Process) the qualifier ‘severity’ combines with a core concept of ‘DILI’ to express the concept ‘the severity level of DILI’ (Disease → (intrinsic) Characteristic/Quality) the qualifier ‘abundance’ combines with a core concept of ‘BRCA2’ to express the concept ‘abundance of BRCA2’ (Gene → (extrinsic) characteristic/quality)" ; @@ -8405,6 +8649,7 @@ biolink:available_from a owl:ObjectProperty ; rdfs:label "available from" ; rdfs:range biolink:DrugAvailabilityEnum ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; skos:inScheme biolink: . biolink:base_coordinate a owl:DatatypeProperty ; @@ -8504,6 +8749,7 @@ biolink:genetically_associated_with a owl:DatatypeProperty, owl:SymmetricProperty ; rdfs:label "genetically associated with" ; rdfs:subPropertyOf biolink:associated_with ; + skos:definition "A statistical association, observed in genetic studies, between a genetic entity such as a gene, locus, or variant and a phenotype, disease, or trait." ; skos:exactMatch WIKIDATA_PROPERTY:P2293 ; skos:inScheme biolink: ; biolink:canonical_predicate true ; @@ -8788,7 +9034,7 @@ biolink:pages a owl:DatatypeProperty ; biolink:part_qualifier a owl:DatatypeProperty ; rdfs:label "part qualifier" ; rdfs:subPropertyOf biolink:qualifier ; - skos:definition "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail)." ; + skos:definition "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it)." ; skos:inScheme biolink: . biolink:physically_interacts_with a owl:DatatypeProperty, @@ -8955,7 +9201,7 @@ biolink:upstream_resource_ids a owl:DatatypeProperty ; rdfs:domain biolink:RetrievalSource ; rdfs:range xsd:anyURI ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact." ; + skos:definition "An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources." ; skos:inScheme biolink: . biolink:Activity a owl:Class ; @@ -8980,46 +9226,47 @@ biolink:Activity a owl:Class ; biolink:AdministrativeEntity a owl:Class ; rdfs:label "administrative entity" ; rdfs:subClassOf biolink:NamedThing ; + skos:definition "An entity that is the byproduct of an administrative process." ; skos:inScheme biolink: . biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], + owl:maxCardinality 1 ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:issue ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:published_in ], + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:issue ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:issue ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:published_in ], biolink:Publication ; skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; skos:exactMatch fabio:article, @@ -9035,6 +9282,7 @@ biolink:Behavior a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalProcess ; + skos:definition "The internally coordinated responses (actions or inactions) of organisms (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." ; skos:exactMatch STY:T053, ; skos:inScheme biolink: ; @@ -9053,47 +9301,48 @@ biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:chapter ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:chapter ], + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:volume ], biolink:Publication ; + skos:definition "A section of a book that forms a discrete unit of a larger published work and may be independently authored or cited." ; skos:inScheme biolink: . biolink:Case a owl:Class ; rdfs:label "case" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sex ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:SubjectOfInvestigation ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_biological_sex ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sex ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalSex ; owl:onProperty biolink:has_biological_sex ], biolink:IndividualOrganism ; skos:altLabel "patient", @@ -9104,12 +9353,14 @@ biolink:Case a owl:Class ; a owl:Class ; rdfs:label "allosteric_modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism that occurs when a chemical exerts an effect on a protein targets via a different binding site than the natural ('orthosteric') ligand site." . a owl:Class ; rdfs:label "immune_system_modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism in which the actions of the effector on the immune system ultimately mediate the affects a target." . a owl:Class ; rdfs:label "methylation" ; @@ -9119,35 +9370,39 @@ biolink:Case a owl:Class ; a owl:Class ; rdfs:label "mixed_allosteric_modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An allosteric modulation mechanism that occurs when a chemical may exert an activating effect or an inhibitory effect in different conditions / contexts (e.g. concentration, receptor conformational state, signaling pathway context, receptor subtype, cellular environment)." . a owl:Class ; rdfs:label "noncompetitive_inhibition" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "An inhibition mechanism in which the effector binds to a target molecule (such as an enzyme) at a site other than the active site, in a way that reduces the activity of the target." . a owl:Class ; rdfs:label "stabilization" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch CHEMBL.MECHANISM:stabiliser ; + skos:definition "A modulation mechanism in which the effector increases the conformational stability of a protein or complex." . biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "cell line to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; skos:inScheme biolink: . @@ -9155,164 +9410,164 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalAffectsBiologicalEntityAssociation a owl:Class ; rdfs:label "chemical affects biological entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:BiologicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalEntity ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a biological entity (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; skos:inScheme biolink: . @@ -9326,10 +9581,10 @@ biolink:ChemicalEntityToEntityAssociationMixin a owl:Class ; biolink:ChemicalExposure a owl:Class ; rdfs:label "chemical exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; + owl:minCardinality 0 ; owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:QuantityValue ; owl:onProperty biolink:has_quantitative_value ], biolink:ExposureEvent ; skos:definition "A chemical exposure is an intake of a particular chemical entity." ; @@ -9372,6 +9627,7 @@ biolink:CodingSequence a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; + skos:definition "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." ; skos:exactMatch , SIO:001390 ; skos:inScheme biolink: . @@ -9394,6 +9650,7 @@ biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a owl:Class ; biolink:DiseaseToEntityAssociationMixin a owl:Class ; rdfs:label "disease to entity association mixin" ; rdfs:subClassOf ; + skos:definition "A mixin applied to any association whose subject (source node) is a disease." ; skos:inScheme biolink: . biolink:DrugExposure a owl:Class ; @@ -9426,6 +9683,7 @@ biolink:FDA_adverse_event_level a owl:ObjectProperty ; rdfs:label "FDA adverse event level" ; rdfs:range biolink:FDAIDAAdverseEventEnum ; rdfs:subPropertyOf biolink:association_slot ; + skos:definition "The level or severity grade of an adverse event as classified by FDA adverse-event terminology, drawn from FDAIDAAdverseEventEnum; used on adverse-event associations." ; skos:inScheme biolink: . biolink:GeneExpressionMixin a owl:Class ; @@ -9440,10 +9698,13 @@ biolink:GeneExpressionMixin a owl:Class ; linkml:PermissibleValue . biolink:GeneToDiseasePredicateEnum a owl:Class ; + rdfs:label "GeneToDiseasePredicateEnum" ; rdfs:subClassOf linkml:EnumDefinition ; - owl:unionOf ( ) ; - linkml:permissible_values , - . + owl:unionOf ( ) ; + skos:definition "Enumeration of predicates permissible for use in gene to disease associations. This constrains the relationship types that can be used between genes and diseases." ; + skos:inScheme biolink: ; + linkml:permissible_values , + . biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; @@ -9451,74 +9712,74 @@ biolink:GenomicSequenceLocalization a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:end_interbase_coordinate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:StrandEnum ; + owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhaseEnum ; - owl:onProperty biolink:phase ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:strand ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:StrandEnum ; - owl:onProperty biolink:strand ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:genome_build ], + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:minCardinality 0 ; + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:phase ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:end_interbase_coordinate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:phase ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:genome_build ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:allValuesFrom biolink:StrandEnum ; owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:start_interbase_coordinate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhaseEnum ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:minCardinality 0 ; + owl:onProperty biolink:start_interbase_coordinate ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -9528,39 +9789,40 @@ biolink:GenomicSequenceLocalization a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; + skos:definition "An association between a genotype and a disease, in which the genotype (typically a combination of alleles at one or more loci) is linked to the disease state." ; skos:inScheme biolink: ; skos:note "TODO decide no how to model pathogenicity" . @@ -9573,22 +9835,22 @@ biolink:GeographicLocation a owl:Class ; rdfs:label "geographic location" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:float ; - owl:onProperty biolink:longitude ], + owl:onProperty biolink:latitude ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:latitude ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:latitude ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:latitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch STY:T083, @@ -9601,7 +9863,6 @@ biolink:Mammal a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:SubjectOfInvestigation ], biolink:CellularOrganism ; - skos:definition "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; skos:exactMatch STY:T015, , , @@ -9633,10 +9894,10 @@ biolink:PairwiseGeneToGeneInteraction a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; @@ -9649,6 +9910,7 @@ biolink:PhenotypicFeatureToEntityAssociationMixin a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FrequencyQuantifier ], biolink:FeatureOrDiseaseQualifiersToEntityMixin ; + skos:definition "A mixin applied to any association whose subject (source node) is a phenotypic feature." ; skos:inScheme biolink: . biolink:Polypeptide a owl:Class ; @@ -9670,42 +9932,43 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:stoichiometry ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:reaction_side ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:reaction_direction ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ReactionDirectionEnum ; + owl:onProperty biolink:reaction_direction ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ReactionDirectionEnum ; - owl:onProperty biolink:reaction_direction ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:reaction_direction ], + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:ReactionSideEnum ; owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:stoichiometry ], biolink:ChemicalEntityToChemicalEntityAssociation ; + skos:definition "An association between a biochemical reaction and a participating molecular entity, qualified by the stoichiometry, the side (reactant vs. product) on which the participant appears, and the direction of the reaction." ; skos:inScheme biolink: . biolink:SequenceAssociation a owl:Class ; @@ -9736,26 +9999,26 @@ biolink:StudyPopulation a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Device ; - owl:onProperty biolink:has_device ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_drug ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_device ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; - owl:onProperty biolink:has_drug ], + owl:allValuesFrom biolink:Procedure ; + owl:onProperty biolink:has_procedure ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Procedure ; - owl:onProperty biolink:has_procedure ], + owl:allValuesFrom biolink:Device ; + owl:onProperty biolink:has_device ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:has_drug ], biolink:ExposureEvent ; skos:altLabel "medical action", "medical intervention" ; @@ -9771,62 +10034,63 @@ biolink:VariantToDiseaseAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; + skos:definition "An association between a sequence variant and a disease, in which the allele state of the variant is linked to the disease state." ; skos:inScheme biolink: ; skos:note "TODO decide no how to model pathogenicity" . biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; skos:inScheme biolink: . @@ -9836,6 +10100,7 @@ biolink:acts_upstream_of_or_within a owl:ObjectProperty ; rdfs:domain biolink:GeneOrGeneProduct ; rdfs:range biolink:BiologicalProcess ; rdfs:subPropertyOf biolink:acts_upstream_of ; + skos:definition "Holds between a gene or gene product and a biological process when the gene product either acts upstream of the process or participates in it; used when the more specific causal relationship is not known. Corresponds to RO:0002264." ; skos:exactMatch RO:0002264 ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -9851,7 +10116,7 @@ biolink:affects_sensitivity_to a owl:ObjectProperty ; rdfs:domain biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - skos:definition "holds between two chemical entities or genes or gene products where the action of one affects the susceptibility/sensitivity of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other." ; + skos:definition "holds between two chemical entities or genes or gene products where the action of one affects the susceptibility/sensitivity of a biological entity or system to the other." ; skos:exactMatch CTD:affects_response_to ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -9898,8 +10163,6 @@ biolink:associated_with_response_to a owl:DatatypeProperty ; rdfs:subPropertyOf biolink:associated_with ; skos:definition "A statistical association used to indicate that the object of a statement using this predicate induces a response of some kind in the subject entity. Intentionally broad in definition, this predicate should be used with qualifiers to narrow the type of response (E.g. whether the response is therapeutic, phenotypic, detrimental, resistant, etc. is captured in context, direction, and aspect qualifiers)." ; skos:inScheme biolink: ; - skos:note """subject: NCBIGene:2064 # HER2 subject_aspect: Amplification predicate: associated with response to object: CHEBI:10035 # Trastuzumab response_type_qualifier: therapeutic_sensitivity response_direction_qualifer: increased response_target_qualifier: human patient disease_context_qualifier: MONDO:0007254 # breast cancer -subject: MONDO:0007254 predicate: associated with response to qualified_predicate: associated with object: CHEBI:10035 # Trastuzumab response_context_qualifier: therapeutic_sensitivity""" ; biolink:canonical_predicate true . biolink:chapter a owl:DatatypeProperty ; @@ -10069,6 +10332,7 @@ biolink:distribution_download_url a owl:DatatypeProperty ; rdfs:label "distribution download url" ; rdfs:domain biolink:DatasetDistribution ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "A URL from which a specific distribution (serialization or format) of a dataset may be directly downloaded; corresponds to dcat:downloadURL specialised for the dataset distribution domain." ; skos:exactMatch dcat:downloadURL ; skos:inScheme biolink: . @@ -10221,6 +10485,7 @@ biolink:format a owl:DatatypeProperty ; rdfs:label "format" ; rdfs:domain biolink:InformationContentEntity ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; skos:exactMatch dct:format, WIKIDATA_PROPERTY:P2701 ; skos:inScheme biolink: . @@ -10263,11 +10528,12 @@ biolink:has_binary_relation a owl:ObjectProperty ; biolink:has_biological_sex a owl:ObjectProperty ; rdfs:label "has biological sex" ; rdfs:range biolink:BiologicalSex ; - skos:definition "The biological sex of the entity (e.g., male or female) regarding a case description from a phenopacket" ; + skos:definition "The biological sex of the entity regarding a case description from a phenopacket" ; skos:inScheme biolink: . biolink:has_chemical_role a owl:ObjectProperty ; rdfs:label "has chemical role" ; + rdfs:domain biolink:ChemicalEntity ; rdfs:range biolink:ChemicalRole ; rdfs:subPropertyOf biolink:related_to_at_concept_level ; owl:inverseOf biolink:is_chemical_role_of ; @@ -10291,6 +10557,7 @@ biolink:has_dataset a owl:ObjectProperty ; rdfs:range biolink:Dataset ; rdfs:subPropertyOf biolink:node_property ; skos:broadMatch dct:source ; + skos:definition "Links a dataset version to the underlying dataset that it is a version of." ; skos:inScheme biolink: . biolink:has_distribution a owl:ObjectProperty ; @@ -10298,6 +10565,7 @@ biolink:has_distribution a owl:ObjectProperty ; rdfs:domain biolink:DatasetVersion ; rdfs:range biolink:DatasetDistribution ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "Links a dataset version to one of its dataset distributions (a specific representation or serialization of the dataset)." ; skos:inScheme biolink: . biolink:has_gene_or_gene_product a owl:ObjectProperty ; @@ -10333,6 +10601,7 @@ biolink:has_taxonomic_rank a owl:ObjectProperty ; rdfs:label "has taxonomic rank" ; rdfs:range biolink:TaxonomicRank ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "The taxonomic rank (e.g. species, genus, family, order, kingdom) assigned to an organism taxon." ; skos:inScheme biolink: ; skos:mappingRelation WIKIDATA:P105 . @@ -10400,6 +10669,7 @@ biolink:ingest_date a owl:DatatypeProperty ; rdfs:domain biolink:DatasetVersion ; rdfs:subPropertyOf biolink:node_property ; skos:broadMatch dct:issued ; + skos:definition "The date on which a dataset version was ingested into the local knowledge graph or downstream data system; a specialization of dct:issued for the ingestion context." ; skos:inScheme biolink: . biolink:inheritance a owl:ObjectProperty ; @@ -10431,12 +10701,14 @@ biolink:is_supplement a owl:DatatypeProperty ; rdfs:label "is supplement" ; rdfs:domain biolink:ChemicalMixture ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food." ; skos:inScheme biolink: . biolink:is_toxic a owl:DatatypeProperty ; rdfs:label "is toxic" ; rdfs:range xsd:boolean ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; skos:inScheme biolink: . biolink:knowledge_level a owl:ObjectProperty ; @@ -10461,6 +10733,7 @@ biolink:license a owl:DatatypeProperty ; rdfs:label "license" ; rdfs:domain biolink:InformationContentEntity ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; skos:exactMatch dct:license ; skos:inScheme biolink: ; skos:narrowMatch WIKIDATA_PROPERTY:P275 . @@ -10631,6 +10904,7 @@ biolink:rights a owl:DatatypeProperty ; rdfs:label "rights" ; rdfs:domain biolink:InformationContentEntity ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; skos:exactMatch dct:rights ; skos:inScheme biolink: . @@ -10645,6 +10919,7 @@ biolink:source_logo a owl:DatatypeProperty ; rdfs:label "source logo" ; rdfs:domain biolink:DatasetSummary ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "A URL referencing an image that serves as the visual logo of a data source." ; skos:inScheme biolink: . biolink:source_web_page a owl:DatatypeProperty ; @@ -10652,6 +10927,7 @@ biolink:source_web_page a owl:DatatypeProperty ; rdfs:domain biolink:DatasetSummary ; rdfs:subPropertyOf biolink:node_property ; skos:broadMatch dct:source ; + skos:definition "A URL of a web page that documents or serves as the landing page for a data source." ; skos:inScheme biolink: . biolink:start_interbase_coordinate a owl:DatatypeProperty ; @@ -10779,6 +11055,7 @@ biolink:trade_name a owl:DatatypeProperty ; rdfs:label "trade name" ; rdfs:domain biolink:ChemicalEntity ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; skos:inScheme biolink: . biolink:treats a owl:ObjectProperty ; @@ -10855,12 +11132,6 @@ biolink:AffinityMeasurement a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:affinity ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:affinity ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AffinityParameterEnum ; - owl:onProperty biolink:affinity_parameter ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:affinity ], @@ -10868,17 +11139,23 @@ biolink:AffinityMeasurement a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:has_binary_relation ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BinaryRelationEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_binary_relation ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:affinity_parameter ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AffinityParameterEnum ; + owl:onProperty biolink:affinity_parameter ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:affinity_parameter ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:BinaryRelationEnum ; owl:onProperty biolink:has_binary_relation ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:affinity ], biolink:NamedThing ; skos:definition "The type of measurement describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the affinity parameter is pIC50 and the affinity value is 8.6. The binary relation, if given, qualifies the affinity as greater than, less than, or equal." ; skos:inScheme biolink: . @@ -10886,7 +11163,11 @@ biolink:AffinityMeasurement a owl:Class ; a owl:Class ; rdfs:label "antagonism" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch DGIdb:antagonist, + CHEMBL.MECHANISM:antagonist ; + skos:definition "An inhibition mechanism in which the effector binds to a receptor and prevents activation by an agonist through competing for the binding site." ; + skos:narrowMatch CHEMBL.MECHANISM:allosteric_antagonist . a owl:Class ; rdfs:label "lipidation" ; @@ -10904,11 +11185,15 @@ biolink:CellLine a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:SubjectOfInvestigation ], biolink:OrganismalEntity ; + skos:definition "A cultured cell population that is genetically stable and homogeneous, sharing a common propagation history through successive passages in culture." ; skos:exactMatch ; skos:inScheme biolink: . biolink:ChemicalEntityDerivativeEnum a owl:Class ; + rdfs:label "ChemicalEntityDerivativeEnum" ; rdfs:subClassOf linkml:EnumDefinition ; + skos:definition "An enumeration of relationships by which one chemical entity is derived from another, e.g., a metabolite produced from a parent compound." ; + skos:inScheme biolink: ; linkml:permissible_values . biolink:ChemicalEntityOrProteinOrPolypeptide a owl:Class ; @@ -10920,41 +11205,41 @@ biolink:ChemicalEntityOrProteinOrPolypeptide a owl:Class ; biolink:ChemicalEntityToChemicalEntityAssociation a owl:Class ; rdfs:label "chemical entity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], biolink:Association ; skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; skos:inScheme biolink: . @@ -10969,13 +11254,6 @@ biolink:ChemicalEntityToChemicalEntityAssociation a owl:Class ; rdfs:subClassOf biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum, . -biolink:ChemicalRole a owl:Class ; - rdfs:label "chemical role" ; - rdfs:subClassOf biolink:Attribute ; - skos:definition "A role played by the molecular entity or part thereof within a chemical context." ; - skos:exactMatch ; - skos:inScheme biolink: . - a owl:Class ; rdfs:label "not_approved_for_condition" ; rdfs:subClassOf biolink:ClinicalApprovalStatusEnum, @@ -11000,8 +11278,11 @@ biolink:DiagnosticAid a owl:Class ; skos:inScheme biolink: . biolink:DrugAvailabilityEnum a owl:Class ; + rdfs:label "DrugAvailabilityEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration describing how a drug or chemical entity may be obtained, distinguishing products that are available over the counter from those that require a prescription." ; + skos:inScheme biolink: ; linkml:permissible_values , . @@ -11027,6 +11308,9 @@ biolink:GeneFamily a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneOrGeneProductOrGeneFamily ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneGroupingMixin ], @@ -11049,7 +11333,8 @@ biolink:GeneFamily a owl:Class ; a owl:Class ; rdfs:label "activity_or_abundance" ; rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Used in cases where the specificity of the relationship can not be determined to be either activity or abundance. In general, a more specific value from this enumeration should be used." . a owl:Class ; rdfs:label "molecular_interaction" ; @@ -11061,15 +11346,12 @@ biolink:GeneFamily a owl:Class ; rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum, linkml:PermissibleValue . -biolink:GeneOrGeneProductOrGeneFamily a owl:Class ; - rdfs:label "gene or gene product or gene family" ; - rdfs:subClassOf ; - skos:definition "A union of gene family or gene loci or gene products, useful to define the association between a gene or gene product or gene family and some other general class of entity (e.g. biological process or anatomical entity)" ; - skos:inScheme biolink: . - biolink:LogicalInterpretationEnum a owl:Class ; + rdfs:label "LogicalInterpretationEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( os:SomeSomeInterpretation os:AllSomeInterpretation ) ; + skos:definition "An enumeration of logical interpretations that can be applied to a triple to indicate whether the relation should be read as existential on both sides (some-some), universal-existential (all-some), or its inverse (inverse all-some)." ; + skos:inScheme biolink: ; linkml:permissible_values os:AllSomeInterpretation, os:SomeSomeInterpretation, . @@ -11098,6 +11380,7 @@ biolink:MaterialSample a owl:Class ; biolink:NoncodingRNAProduct a owl:Class ; rdfs:label "noncoding RNA product" ; rdfs:subClassOf biolink:RNAProduct ; + skos:definition "An RNA transcript that does not encode for a protein rather the RNA molecule is the functional gene product." ; skos:exactMatch , SIO:001235 ; skos:inScheme biolink: . @@ -11105,26 +11388,26 @@ biolink:NoncodingRNAProduct a owl:Class ; biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], biolink:Association ; skos:definition "A relationship between two organism taxon nodes" ; skos:inScheme biolink: . @@ -11150,7 +11433,8 @@ biolink:Procedure a owl:Class ; skos:narrowMatch STY:T059, STY:T060, STY:T061, - STY:T063 . + STY:T063, + MAXO:0000001 . biolink:RNAProduct a owl:Class ; rdfs:label "RNA product" ; @@ -11158,13 +11442,17 @@ biolink:RNAProduct a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneProductMixin ], biolink:Transcript ; + skos:definition "High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds typically synthesized by a DNA- or RNA-dependent RNA polymerase that constitutes the product of a gene. Distinct in emphasis from `biolink:Transcript`, which denotes the informational output of transcription at the gene-model level rather than the chemical species itself." ; skos:exactMatch , WIKIDATA:Q11053 ; skos:inScheme biolink: . biolink:ReactionSideEnum a owl:Class ; + rdfs:label "ReactionSideEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration indicating on which side of a biochemical reaction a participant appears - the left-hand (reactant/substrate) side or the right-hand (product) side, as written." ; + skos:inScheme biolink: ; linkml:permissible_values , . @@ -11172,13 +11460,13 @@ biolink:RegulatoryRegion a owl:Class ; rdfs:label "regulatory region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], @@ -11193,11 +11481,15 @@ biolink:RegulatoryRegion a owl:Class ; biolink:RelationshipQuantifier a owl:Class ; rdfs:label "relationship quantifier" ; rdfs:subClassOf ; + skos:definition "A mixin for quantifying aspects of the strength, frequency, or specificity of a relationship between two entities." ; skos:inScheme biolink: . biolink:ResponseEnum a owl:Class ; + rdfs:label "ResponseEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "A response to a treatment or intervention" ; + skos:inScheme biolink: ; linkml:permissible_values , . @@ -11206,6 +11498,7 @@ biolink:acts_upstream_of a owl:ObjectProperty ; rdfs:domain biolink:GeneOrGeneProduct ; rdfs:range biolink:BiologicalProcess ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; + skos:definition "Holds between a gene or gene product and a biological process such that the molecular function of the gene product, by way of a chain of causally linked events, is upstream of and contributes to the execution of the process." ; skos:exactMatch RO:0002263 ; skos:inScheme biolink: ; biolink:canonical_predicate true . @@ -11228,6 +11521,7 @@ biolink:affects_likelihood_of a owl:DatatypeProperty ; biolink:aggregate_statistic a owl:DatatypeProperty ; rdfs:label "aggregate statistic" ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "An abstract grouping for summary numerical measures (e.g. count, total, quotient, percentage, rate) computed over a set of observations or a reference population, used to describe a property of an aggregated entity rather than an individual instance." ; skos:inScheme biolink: . biolink:broad_match a owl:DatatypeProperty ; @@ -11526,29 +11820,33 @@ biolink:temporal_context_qualifier a owl:DatatypeProperty ; biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], biolink:Association ; + skos:definition "An abstract parent class for associations between two anatomical entities, such as part-of, develops-from, or other mereological and ontogenic relationships." ; skos:inScheme biolink: . biolink:BinaryRelationEnum a owl:Class ; + rdfs:label "BinaryRelationEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "Mathematical binary relation qualifiers of a value in its context." ; + skos:inScheme biolink: ; linkml:permissible_values , , . @@ -11562,7 +11860,12 @@ biolink:CaseToEntityAssociationMixin a owl:Class ; a owl:Class ; rdfs:label "agonism" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch DGIdb:agonist, + CHEMBL.MECHANISM:agonist ; + skos:definition "An activation mechanism in which the effector binds and activates a receptor to mimic the effect of an endogenous ligand." ; + skos:narrowMatch DGIdb:partial_agonist, + CHEMBL.MECHANISM:partial_agonist . biolink:CellularComponent a owl:Class ; rdfs:label "cellular component" ; @@ -11577,14 +11880,25 @@ biolink:CellularComponent a owl:Class ; WIKIDATA:Q5058355 ; skos:inScheme biolink: . +biolink:ChemicalRole a owl:Class ; + rdfs:label "chemical role" ; + rdfs:subClassOf biolink:Attribute ; + skos:definition "A role played by the molecular entity or part thereof within a chemical context." ; + skos:exactMatch ; + skos:inScheme biolink: . + biolink:ClinicalIntervention a owl:Class ; rdfs:label "clinical intervention" ; rdfs:subClassOf biolink:ClinicalEntity ; + skos:definition "A medical procedure, treatment, or action taken by healthcare professionals to modify the course of a disease or condition." ; skos:inScheme biolink: . biolink:ClinicalTrialAgeStageEnum a owl:Class ; + rdfs:label "ClinicalTrialAgeStageEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "Enumeration of age stages or populations commonly used in clinical trials to categorize participant demographics and target populations." ; + skos:inScheme biolink: ; linkml:permissible_values , , . @@ -11595,10 +11909,10 @@ biolink:DatasetDistribution a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:distribution_download_url ], biolink:InformationContentEntity ; skos:definition "an item that holds distribution level information about a dataset." ; @@ -11609,22 +11923,22 @@ biolink:DatasetSummary a owl:Class ; rdfs:label "dataset summary" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:source_web_page ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:source_web_page ], + owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:source_logo ], + owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_web_page ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:source_web_page ], biolink:InformationContentEntity ; skos:definition "an item that holds summary level information about a dataset." ; skos:inScheme biolink: . @@ -11637,6 +11951,7 @@ biolink:DatasetSummary a owl:Class ; biolink:FrequencyQuantifier a owl:Class ; rdfs:label "frequency quantifier" ; rdfs:subClassOf biolink:RelationshipQuantifier ; + skos:definition "A relationship quantifier that expresses how often a relationship holds, using count, total, quotient, or percentage measures." ; skos:inScheme biolink: . biolink:GeneProductIsoformMixin a owl:Class ; @@ -11648,103 +11963,104 @@ biolink:GeneProductIsoformMixin a owl:Class ; biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:gene2phenotype_confidence_category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneToDiseasePredicateEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( xsd:string [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^HP:\\d{7}$" ] ) ] ) ] ; + owl:minCardinality 0 ; owl:onProperty biolink:allelic_requirement ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:diseases_confidence_score ], + owl:maxCardinality 1 ; + owl:onProperty biolink:gene2phenotype_confidence_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:allelic_requirement ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:diseases_confidence_score ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:gene2phenotype_confidence_category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:diseases_confidence_score ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( xsd:string [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^HP:\\d{7}$" ] ) ] ) ] ; owl:onProperty biolink:allelic_requirement ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:diseases_confidence_score ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:gene2phenotype_confidence_category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:diseases_confidence_score ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneToDiseasePredicateEnum ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:gene2phenotype_confidence_category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:allelic_requirement ], + owl:onProperty biolink:diseases_confidence_score ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:gene2phenotype_confidence_category ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], biolink:Association ; skos:closeMatch dcid:DiseaseGeneAssociation ; + skos:definition "An association between a gene or gene product and a disease, where variation in the gene is correlated with the disease." ; skos:exactMatch SIO:000983 ; skos:inScheme biolink: ; skos:note "NCIT:R176 refers to the inverse relationship", @@ -11755,19 +12071,19 @@ biolink:GeneToGeneAssociation a owl:Class ; rdfs:label "gene to gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -11777,12 +12093,15 @@ biolink:GeneToGeneAssociation a owl:Class ; skos:inScheme biolink: . biolink:GeneToPhenotypicFeaturePredicateEnum a owl:Class ; + rdfs:label "GeneToPhenotypicFeaturePredicateEnum" ; rdfs:subClassOf linkml:EnumDefinition ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . + owl:unionOf ( ) ; + skos:definition "Enumeration of predicates permissible for use in gene to phenotypic feature associations. This constrains the relationship types that can be used between genes and phenotypic features." ; + skos:inScheme biolink: ; + linkml:permissible_values , + , + , + . biolink:IndividualOrganism a owl:Class ; rdfs:label "individual organism" ; @@ -11791,7 +12110,7 @@ biolink:IndividualOrganism a owl:Class ; owl:someValuesFrom biolink:SubjectOfInvestigation ], biolink:OrganismalEntity ; skos:altLabel "organism" ; - skos:definition "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; + skos:definition "An instance of an organism. For example, Charles Darwin, my pet cat." ; skos:exactMatch STY:T001, SIO:010000 ; skos:inScheme biolink: ; @@ -11815,6 +12134,7 @@ biolink:Pathway a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalProcess ; + skos:definition "A hierarchical ordering of connected molecular reactions (steps) that represent a specific biological process, such as signaling or metabolism." ; skos:exactMatch , WIKIDATA:Q4915012 ; skos:inScheme biolink: ; @@ -11822,8 +12142,11 @@ biolink:Pathway a owl:Class ; SIO:010526 . biolink:PhaseEnum a owl:Class ; + rdfs:label "PhaseEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "phase" ; + skos:inScheme biolink: ; linkml:permissible_values , , . @@ -11852,30 +12175,33 @@ biolink:Protein a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:has_unit ], - [ a owl:Restriction ; owl:allValuesFrom xsd:double ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_numeric_value ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty biolink:has_unit ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_unit ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_numeric_value ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_unit ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; skos:inScheme biolink: . biolink:ResourceRoleEnum a owl:Class ; + rdfs:label "ResourceRoleEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience." ; + skos:inScheme biolink: ; linkml:permissible_values , , . @@ -11883,23 +12209,23 @@ biolink:ResourceRoleEnum a owl:Class ; biolink:SequenceFeatureRelationship a owl:Class ; rdfs:label "sequence feature relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; skos:exactMatch CHADO:feature_relationship ; @@ -11913,6 +12239,7 @@ biolink:VariantToEntityAssociationMixin a owl:Class ; biolink:Zygosity a owl:Class ; rdfs:label "zygosity" ; rdfs:subClassOf biolink:Attribute ; + skos:definition "An allelic state describing the degree of similarity between features at a single locus, specifically whether alleles at the same location on paired chromosomes are identical or different." ; skos:exactMatch ; skos:inScheme biolink: . @@ -11927,6 +12254,7 @@ biolink:contributor a owl:ObjectProperty ; rdfs:domain biolink:Agent ; rdfs:range biolink:InformationContentEntity ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; + skos:definition "Links an information content entity (such as a dataset, publication, or software artefact) to an agent responsible for making contributions to it. Used as an abstract grouping predicate over more specific contribution roles (author, editor, publisher, provider). Corresponds to dct:contributor." ; skos:exactMatch dct:contributor ; skos:inScheme biolink: ; skos:note "This is a grouping for predicates relating entities to their associated contributors realizing them" . @@ -12013,17 +12341,20 @@ biolink:sequence_localization_attribute a owl:DatatypeProperty ; a owl:Class ; rdfs:label "automated_agent" ; rdfs:subClassOf biolink:AgentTypeEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "An automated agent, typically a software program or tool, that is responsible for generating a statement of knowledge. Human contribution to the knowledge creation process ends with the definition and coding of algorithms or analysis pipelines that get executed by the automated agent." . a owl:Class ; rdfs:label "covalent_binding" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism mediated by a direct covalent binding interaction between effector and target chemical or biomolecular entity." . a owl:Class ; rdfs:label "positive_modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism that positively effects the normal functioning of a target by increasing or enhancing its activity or abundance, or its sensitivity to other factors that do so." . a owl:Class ; rdfs:label "genetic_variant_form" ; @@ -12042,27 +12373,27 @@ biolink:DatasetVersion a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_distribution ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:ingest_date ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Dataset ; + owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_distribution ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DatasetDistribution ; + owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:ingest_date ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Dataset ; - owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_dataset ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:ingest_date ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DatasetDistribution ; - owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:ingest_date ], @@ -12071,8 +12402,11 @@ biolink:DatasetVersion a owl:Class ; skos:inScheme biolink: . biolink:DruggableGeneCategoryEnum a owl:Class ; + rdfs:label "DruggableGeneCategoryEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration of druggability categories for gene targets as defined by the IDG (Illuminating the Druggable Genome) / Pharos target development level classification: Tclin (targets of approved drugs), Tchem (targets with potent bioactives), Tbio (targets with biological knowledge), and Tdark (poorly characterized targets)." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -12085,8 +12419,11 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a owl:Class ; skos:inScheme biolink: . biolink:FDAIDAAdverseEventEnum a owl:Class ; + rdfs:label "FDAIDAAdverseEventEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32" ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -12101,22 +12438,22 @@ biolink:FrequencyQualifierMixin a owl:Class ; biolink:FunctionalAssociation a owl:Class ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; @@ -12128,6 +12465,12 @@ biolink:GeneGroupingMixin a owl:Class ; skos:definition "any grouping of multiple genes or gene products" ; skos:inScheme biolink: . +biolink:GeneOrGeneProductOrGeneFamily a owl:Class ; + rdfs:label "gene or gene product or gene family" ; + rdfs:subClassOf biolink:MacromolecularMachineMixin ; + skos:definition "A union of gene family or gene loci or gene products, useful to define the association between a gene or gene product or gene family and some other general class of entity." ; + skos:inScheme biolink: . + biolink:ModelToDiseaseAssociationMixin a owl:Class ; rdfs:label "model to disease association mixin" ; rdfs:subClassOf ; @@ -12154,17 +12497,23 @@ biolink:PhysicalEntity a owl:Class ; skos:narrowMatch STY:T073 . biolink:ReactionDirectionEnum a owl:Class ; + rdfs:label "ReactionDirectionEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration of possible directions for a biochemical reaction, indicating whether it proceeds left-to-right, right-to-left, is bidirectional (reversible), or has no net direction." ; + skos:inScheme biolink: ; linkml:permissible_values , , , . biolink:ResponseTargetEnum a owl:Class ; + rdfs:label "ResponseTargetEnum" ; rdfs:subClassOf linkml:EnumDefinition ; - owl:unionOf ( ) ; - linkml:permissible_values , + owl:unionOf ( ) ; + skos:definition "The target of a treatment or intervention" ; + skos:inScheme biolink: ; + linkml:permissible_values , , , . @@ -12172,10 +12521,10 @@ biolink:ResponseTargetEnum a owl:Class ; biolink:Study a owl:Class ; rdfs:label "study" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:StudyResult ; + owl:minCardinality 0 ; owl:onProperty biolink:has_study_results ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:StudyResult ; owl:onProperty biolink:has_study_results ], biolink:Activity ; skos:closeMatch , @@ -12320,6 +12669,7 @@ biolink:has_zygosity a owl:ObjectProperty ; rdfs:domain biolink:NucleicAcidEntity ; rdfs:range biolink:Zygosity ; rdfs:subPropertyOf biolink:node_property ; + skos:definition "The zygosity characterising a genotype or nucleic acid entity at a particular locus." ; skos:inScheme biolink: . biolink:iri a owl:DatatypeProperty ; @@ -12406,7 +12756,7 @@ biolink:published_in a owl:DatatypeProperty ; rdfs:domain biolink:Publication ; rdfs:range xsd:anyURI ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "CURIE identifier of a broader publication context within which the publication may be placed, e.g. a specified book or journal." ; + skos:definition "CURIE identifier of a broader publication context within which the publication may be placed." ; skos:exactMatch WIKIDATA_PROPERTY:P1433 ; skos:inScheme biolink: . @@ -12573,7 +12923,10 @@ biolink:supporting_study_metadata a owl:DatatypeProperty ; a owl:Class ; rdfs:label "activation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch DGIdb:activator, + CHEMBL.MECHANISM:activator ; + skos:definition "A positive modulation mechanism in which the effector binds to and positively affects the normal functioning of its target." . biolink:CellularOrganism a owl:Class ; rdfs:label "cellular organism" ; @@ -12581,41 +12934,43 @@ biolink:CellularOrganism a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:SubjectOfInvestigation ], biolink:OrganismalEntity ; + skos:definition "An organism that contains one or more cells belonging to the cellular lineages of life (Archaea, Bacteria, or Eukaryota), whose body consists of one or more cells. Distinguished from acellular biological entities such as viruses and viroids." ; skos:exactMatch ; - skos:inScheme biolink: . + skos:inScheme biolink: ; + skos:note "see: https://github.com/OBOFoundry/COB/pull/211" . biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:highest_FDA_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; owl:allValuesFrom biolink:ApprovalStatusEnum ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ApprovalStatusEnum ; - owl:onProperty biolink:highest_FDA_approval_status ], + owl:minCardinality 0 ; + owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ApprovalStatusEnum ; owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:is_supplement ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -12647,7 +13002,7 @@ biolink:GeneticInheritance a owl:Class ; rdfs:subClassOf biolink:BiologicalEntity ; skos:altLabel "inheritance" ; skos:closeMatch STY:T045 ; - skos:definition "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; + skos:definition "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next." ; skos:exactMatch , , ; @@ -12656,29 +13011,20 @@ biolink:GeneticInheritance a owl:Class ; biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_output ], + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:enabled_by ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], @@ -12687,7 +13033,16 @@ biolink:MolecularActivity a owl:Class ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:has_input ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:enabled_by ], biolink:BiologicalProcessOrActivity ; skos:altLabel "molecular event", "molecular function", @@ -12846,24 +13201,22 @@ biolink:Dataset a owl:Class ; dcid:Dataset ; skos:inScheme biolink: . -biolink:MacromolecularMachineMixin a owl:Class ; - rdfs:label "macromolecular machine mixin" ; - rdfs:subClassOf ; - skos:definition "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; - skos:inScheme biolink: . - a owl:Class ; rdfs:label "clinical_trial_phase" ; rdfs:subClassOf biolink:ResearchPhaseEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer." . biolink:StrandEnum a owl:Class ; + rdfs:label "StrandEnum" ; rdfs:subClassOf linkml:EnumDefinition ; - owl:unionOf ( ) ; - linkml:permissible_values , + owl:unionOf ( ) ; + skos:definition "strand" ; + skos:inScheme biolink: ; + linkml:permissible_values , + , , - , - . + . biolink:has_attribute a owl:ObjectProperty ; rdfs:label "has attribute" ; @@ -13004,6 +13357,7 @@ biolink:synonym a owl:DatatypeProperty ; biolink:BiologicalSex a owl:Class ; rdfs:label "biological sex" ; rdfs:subClassOf biolink:Attribute ; + skos:definition "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved." ; skos:exactMatch ; skos:inScheme biolink: . @@ -13011,10 +13365,10 @@ biolink:Drug a owl:Class ; rdfs:label "drug" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], biolink:MolecularMixture ; skos:broadMatch STY:T121 ; skos:definition "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; @@ -13027,8 +13381,11 @@ biolink:Drug a owl:Class ; skos:note "The CHEBI ID represents a role rather than a substance" . biolink:DrugDeliveryEnum a owl:Class ; + rdfs:label "DrugDeliveryEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration of routes by which a drug is administered or delivered to a patient, including inhalation, oral, transdermal absorption, and various forms of injection (intravenous, subcutaneous, intramuscular)." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -13043,25 +13400,26 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FrequencyQuantifier ], biolink:EntityToFeatureOrDiseaseQualifiersMixin ; + skos:definition "A mixin applied to any association whose object (target node) is a phenotypic feature." ; skos:inScheme biolink: . biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_zygosity ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Zygosity ; - owl:onProperty biolink:has_zygosity ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Zygosity ; + owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], @@ -13073,8 +13431,11 @@ biolink:Genotype a owl:Class ; skos:note "Consider renaming as genotypic entity" . biolink:KnowledgeLevelEnum a owl:Class ; + rdfs:label "KnowledgeLevelEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration characterizing the type of knowledge expressed in a statement and the kind of evidence and reasoning that supports it, as defined by the Translator Knowledge Level / Agent Type (KL/AT) standard. Values include knowledge assertion, logical entailment, prediction, statistical association, text co-occurrence, direct observation, and not-provided." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -13083,6 +13444,12 @@ biolink:KnowledgeLevelEnum a owl:Class ; , . +biolink:MacromolecularMachineMixin a owl:Class ; + rdfs:label "macromolecular machine mixin" ; + rdfs:subClassOf ; + skos:definition "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; + skos:inScheme biolink: . + biolink:PopulationOfIndividualOrganisms a owl:Class ; rdfs:label "population of individual organisms" ; rdfs:subClassOf [ a owl:Restriction ; @@ -13165,6 +13532,7 @@ biolink:timepoint a owl:DatatypeProperty ; biolink:type a owl:DatatypeProperty ; rdfs:label "type" ; rdfs:domain biolink:Entity ; + skos:definition "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; skos:exactMatch gff3:type, gpi:DB_Object_Type ; skos:inScheme biolink: . @@ -13178,8 +13546,11 @@ biolink:volume a owl:DatatypeProperty ; skos:inScheme biolink: . biolink:AffinityParameterEnum a owl:Class ; + rdfs:label "AffinityParameterEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "The types of parameters that can be used to describe the affinity between two entities, characteristically chemicals and proteins. The values are generally stated as the negative base 10 logarithm of the raw measurements." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -13190,8 +13561,11 @@ biolink:AffinityParameterEnum a owl:Class ; . biolink:AgentTypeEnum a owl:Class ; + rdfs:label "AgentTypeEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration of agent types responsible for generating a statement of knowledge, as defined by the Translator Knowledge Level / Agent Type (KL/AT) standard. Values distinguish human (manual) agents from automated agents (including data analysis pipelines, computational models, text-mining agents, image-processing agents) and mixed cases such as manual validation of automated output." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -13204,16 +13578,33 @@ biolink:AgentTypeEnum a owl:Class ; a owl:Class ; rdfs:label "inhibition" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:closeMatch SEMMEDDB:INHIBITS, + DGIdb:inhibitor ; + skos:definition "A negative modulation mechanism in which the effector binds to the target and negatively effects its normal function, e.g. prevention of enzymatic reaction or activation of downstream pathway." ; + skos:narrowMatch DGIdb:blocker, + DGIdb:channel_blocker, + DGIdb:gating_inhibitor, + DGIdb:negative_modulator, + CHEMBL.MECHANISM:antisense_inhibitor, + CHEMBL.MECHANISM:blocker, + CHEMBL.MECHANISM:inhibitor, + CHEMBL.MECHANISM:negative_allosteric_modulator, + CHEMBL.MECHANISM:negative_modulator . a owl:Class ; rdfs:label "negative_modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . + ; + skos:definition "A modulation mechanism that negatively effects the normal functioning of a target by decreasing or impeding its activity or abundance, or its sensitivity to other factors that do so." ; + skos:narrowMatch DGIdb:negative_modulator . biolink:ClinicalApprovalStatusEnum a owl:Class ; + rdfs:label "ClinicalApprovalStatusEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration describing whether a chemical or therapy is approved for use in treating a specific condition (e.g., FDA-approved for a condition, not approved, off-label use, or withdrawn following approval)." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -13224,7 +13615,7 @@ biolink:ClinicalApprovalStatusEnum a owl:Class ; biolink:Outcome a owl:Class ; rdfs:label "outcome" ; rdfs:subClassOf ; - skos:definition "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes." ; + skos:definition "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological outcomes." ; skos:inScheme biolink: . biolink:PhenotypicFeature a owl:Class ; @@ -13237,7 +13628,7 @@ biolink:PhenotypicFeature a owl:Class ; "trait" ; skos:broadMatch , ; - skos:definition "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; + skos:definition "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual often resulting from the interaction of its genotype with its molecular and physical environment." ; skos:exactMatch MESH:D010641, , , @@ -13263,40 +13654,40 @@ biolink:PhenotypicFeature a owl:Class ; biolink:RetrievalSource a owl:Class ; rdfs:label "retrieval source" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:resource_id ], + [ a owl:Restriction ; owl:allValuesFrom biolink:ResourceRoleEnum ; owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:upstream_resource_ids ], + owl:minCardinality 1 ; + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:source_record_urls ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:resource_role ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 1 ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:resource_id ], + owl:minCardinality 0 ; + owl:onProperty biolink:source_record_urls ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:source_record_urls ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 0 ; owl:onProperty biolink:upstream_resource_ids ], biolink:InformationContentEntity ; skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; @@ -13312,10 +13703,10 @@ biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], @@ -13355,14 +13746,14 @@ biolink:xref a owl:DatatypeProperty ; biolink:OrganismalEntity a owl:Class ; rdfs:label "organismal entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SubjectOfInvestigation ], biolink:BiologicalEntity ; skos:definition "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; skos:exactMatch , @@ -13392,14 +13783,14 @@ biolink:anatomical_context_qualifier a owl:DatatypeProperty ; rdfs:label "anatomical context qualifier" ; rdfs:subPropertyOf biolink:statement_qualifier ; skos:definition "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - skos:editorialNote "Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ combines with a core concept of ‘neuron’ to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." ; + skos:editorialNote "Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ combines with a core concept of ‘neuron’ to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies taxonomic context. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." ; skos:inScheme biolink: . biolink:causal_mechanism_qualifier a owl:ObjectProperty ; rdfs:label "causal mechanism qualifier" ; rdfs:range biolink:CausalMechanismQualifierEnum ; rdfs:subPropertyOf biolink:statement_qualifier ; - skos:definition "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + skos:definition "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" ; skos:inScheme biolink: . biolink:object_form_or_variant_qualifier a owl:DatatypeProperty ; @@ -13411,7 +13802,7 @@ biolink:object_form_or_variant_qualifier a owl:DatatypeProperty ; biolink:object_part_qualifier a owl:DatatypeProperty ; rdfs:label "object part qualifier" ; rdfs:subPropertyOf biolink:part_qualifier ; - skos:definition "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + skos:definition "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement)." ; skos:inScheme biolink: . biolink:subject_derivative_qualifier a owl:DatatypeProperty ; @@ -13423,81 +13814,84 @@ biolink:subject_derivative_qualifier a owl:DatatypeProperty ; biolink:subject_part_qualifier a owl:DatatypeProperty ; rdfs:label "subject part qualifier" ; rdfs:subPropertyOf biolink:part_qualifier ; - skos:definition "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + skos:definition "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement)." ; skos:inScheme biolink: . biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:onProperty biolink:description ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; + owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:description ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:description ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:description ], + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:category ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iri ], + owl:maxCardinality 1 ; + owl:onProperty biolink:description ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:onProperty biolink:deprecated ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:deprecated ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_attribute ], + owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:deprecated ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Attribute ; + owl:onProperty biolink:has_attribute ], linkml:ClassDefinition ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; skos:inScheme biolink: . biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; + rdfs:label "GeneOrGeneProductOrChemicalPartQualifierEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration used as a qualifier to indicate a particular structural or functional part of a gene, gene product, or chemical (e.g., 3' UTR, 5' UTR, poly-A tail, promoter, enhancer, exon, or intron)." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -13509,49 +13903,49 @@ biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:has_attribute_type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_attribute_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_qualitative_value ], + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], biolink:NamedThing ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; @@ -13561,29 +13955,26 @@ biolink:Attribute a owl:Class ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:affiliation ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:address ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:address ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:affiliation ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:address ], @@ -13591,8 +13982,11 @@ biolink:Agent a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:affiliation ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -13609,122 +14003,122 @@ biolink:Agent a owl:Class ; biolink:ClinicalTrial a owl:Class ; rdfs:label "clinical trial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalIntervention ; - owl:onProperty biolink:clinical_trial_interventions ], + owl:allValuesFrom biolink:ResearchPhaseEnum ; + owl:onProperty biolink:clinical_trial_phase ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_primary_purpose ], + owl:allValuesFrom biolink:ClinicalTrialStatusEnum ; + owl:onProperty biolink:clinical_trial_overall_status ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_overall_status ], + owl:onProperty biolink:clinical_trial_brief_title ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:clinical_trial_age_range ], + owl:onProperty biolink:clinical_trial_start_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_conditions ], + owl:onProperty biolink:clinical_trial_interventions ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_trial_age_range ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_age_range ], + owl:onProperty biolink:clinical_trial_primary_purpose ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:clinical_trial_start_date ], + owl:onProperty biolink:clinical_trial_primary_purpose ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:clinical_trial_enrollment ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:clinical_trial_brief_title ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:date ; + owl:onProperty biolink:creation_date ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:clinical_trial_intervention_model ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:clinical_trial_phase ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_age_stage ], + owl:onProperty biolink:clinical_trial_start_date ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:clinical_trial_enrollment ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:clinical_trial_tested_intervention ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_brief_title ], + owl:onProperty biolink:clinical_trial_enrollment_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:creation_date ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:clinical_trial_enrollment ], + owl:onProperty biolink:clinical_trial_age_range ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:clinical_trial_overall_status ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:clinical_trial_conditions ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:clinical_trial_tested_intervention ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:clinical_trial_brief_title ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_interventions ], + owl:onProperty biolink:clinical_trial_phase ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:clinical_trial_intervention_model ], + owl:onProperty biolink:clinical_trial_age_range ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:clinical_trial_primary_purpose ], + owl:minCardinality 0 ; + owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_trial_enrollment_type ], + owl:onProperty biolink:clinical_trial_start_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:clinical_trial_intervention_model ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_enrollment_type ], + owl:onProperty biolink:clinical_trial_primary_purpose ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_phase ], + owl:onProperty biolink:clinical_trial_overall_status ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_trial_primary_purpose ], + owl:minCardinality 0 ; + owl:onProperty biolink:clinical_trial_age_stage ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_trial_phase ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:clinical_trial_enrollment ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:clinical_trial_tested_intervention ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:clinical_trial_brief_title ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_start_date ], + owl:onProperty biolink:clinical_trial_age_range ], [ a owl:Restriction ; - owl:allValuesFrom xsd:date ; - owl:onProperty biolink:creation_date ], + owl:minCardinality 0 ; + owl:onProperty biolink:clinical_trial_intervention_model ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:clinical_trial_tested_intervention ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ClinicalIntervention ; + owl:onProperty biolink:clinical_trial_interventions ], [ a owl:Restriction ; owl:allValuesFrom biolink:ClinicalTrialAgeStageEnum ; owl:onProperty biolink:clinical_trial_age_stage ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ResearchPhaseEnum ; - owl:onProperty biolink:clinical_trial_phase ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_tested_intervention ], + owl:onProperty biolink:clinical_trial_conditions ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:clinical_trial_enrollment_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_trial_start_date ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalTrialStatusEnum ; - owl:onProperty biolink:clinical_trial_overall_status ], + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:clinical_trial_conditions ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_trial_tested_intervention ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:clinical_trial_intervention_model ], + owl:onProperty biolink:clinical_trial_enrollment_type ], biolink:Study ; skos:definition "A clinical trial is a research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes." ; skos:exactMatch , @@ -13732,8 +14126,12 @@ biolink:ClinicalTrial a owl:Class ; skos:inScheme biolink: . biolink:ClinicalTrialStatusEnum a owl:Class ; + rdfs:label "ClinicalTrialStatusEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition """Enumeration of clinical trial statuses indicating the recruitment state, availability, or regulatory status of a clinical study or intervention. +""" ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -13755,8 +14153,11 @@ biolink:PhysicalEssence a owl:Class ; skos:inScheme biolink: . biolink:ResearchPhaseEnum a owl:Class ; + rdfs:label "ResearchPhaseEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration of research phases describing the stage of investigation for a drug or therapy, spanning preclinical research through clinical trial phases 1 through 4 (including phase 1/2 and phase 2/3 combinations)." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -13784,11 +14185,13 @@ biolink:name a owl:DatatypeProperty ; biolink:object_context_qualifier a owl:DatatypeProperty ; rdfs:label "object context qualifier" ; rdfs:subPropertyOf biolink:context_qualifier ; + skos:definition "A qualifier describing the context in which the object of an association holds." ; skos:inScheme biolink: . biolink:subject_context_qualifier a owl:DatatypeProperty ; rdfs:label "subject context qualifier" ; rdfs:subPropertyOf biolink:context_qualifier ; + skos:definition "A qualifier describing the context in which the subject of an association holds." ; skos:inScheme biolink: . biolink:Occurrent a owl:Class ; @@ -13799,8 +14202,11 @@ biolink:Occurrent a owl:Class ; skos:inScheme biolink: . biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum a owl:Class ; + rdfs:label "ChemicalOrGeneOrGeneProductFormOrVariantEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration used as a qualifier to indicate a specific form or variant of a chemical, gene, or gene product involved in an association (e.g., modified form, loss-of-function variant, gain-of-function variant, dominant-negative variant, polymorphic form, SNP form, mutant form, or analog form)." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -13818,7 +14224,7 @@ biolink:Disease a owl:Class ; skos:altLabel "condition", "disorder", "medical condition" ; - skos:definition "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; + skos:definition "A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury." ; skos:exactMatch STY:T047, , , @@ -13842,8 +14248,11 @@ biolink:qualifier a owl:DatatypeProperty ; skos:inScheme biolink: . biolink:ApprovalStatusEnum a owl:Class ; + rdfs:label "ApprovalStatusEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration of regulatory and development milestones for a drug or therapeutic, spanning discovery, preclinical research, FDA clinical trial phases (1-4), special review designations (e.g., fast track, breakthrough therapy, priority review), regular FDA approval, and post-approval withdrawal." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -13863,35 +14272,35 @@ biolink:ApprovalStatusEnum a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:PhysicalEntity ; - owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_output ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_input ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:Occurrent ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhysicalEntity ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], @@ -13902,17 +14311,17 @@ biolink:BiologicalProcessOrActivity a owl:Class ; biolink:MolecularEntity a owl:Class ; rdfs:label "molecular entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:is_metabolite ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:is_metabolite ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], biolink:ChemicalEntity ; skos:definition "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; skos:inScheme biolink: ; @@ -13955,41 +14364,41 @@ biolink:BiologicalProcess a owl:Class ; biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:license ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:format ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:date ; + owl:minCardinality 0 ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:rights ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:license ], + owl:onProperty biolink:format ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:format ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:rights ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:creation_date ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:format ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:rights ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:date ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:license ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:creation_date ], + owl:onProperty biolink:license ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:rights ], + owl:maxCardinality 1 ; + owl:onProperty biolink:license ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -14013,10 +14422,10 @@ biolink:InformationContentEntity a owl:Class ; biolink:OrganismTaxon a owl:Class ; rdfs:label "organism taxon" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; owl:allValuesFrom biolink:TaxonomicRank ; @@ -14035,97 +14444,97 @@ biolink:ExposureEvent a owl:Class ; rdfs:label "exposure event" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:exposure_duration ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:exposure_start_age ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:exposure_type ], + owl:onProperty biolink:exposure_vehicle ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:exposure_route ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:exposure_end_age ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:exposure_vehicle ], + owl:maxCardinality 1 ; + owl:onProperty biolink:exposure_magnitude ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:exposure_duration ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:exposure_magnitude ], + owl:onProperty biolink:exposure_route ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exposure_vehicle ], + owl:onProperty biolink:exposure_end_age ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:maxCardinality 1 ; + owl:onProperty biolink:exposure_route ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], + owl:onProperty biolink:exposure_vehicle ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:exposure_magnitude ], + owl:minCardinality 0 ; + owl:onProperty biolink:exposure_duration ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:exposure_route ], + owl:onProperty biolink:exposure_additional_condition ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exposure_duration ], + owl:onProperty biolink:exposure_magnitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:exposure_start_age ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:exposure_additional_condition ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exposure_start_age ], + owl:onProperty biolink:exposure_additional_condition ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; + owl:maxCardinality 1 ; owl:onProperty biolink:exposure_end_age ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:exposure_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:exposure_duration ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:exposure_additional_condition ], + owl:maxCardinality 1 ; + owl:onProperty biolink:exposure_vehicle ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exposure_type ], + owl:onProperty biolink:exposure_start_age ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exposure_additional_condition ], + owl:onProperty biolink:exposure_route ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:exposure_end_age ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:exposure_start_age ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:exposure_magnitude ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:exposure_duration ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:exposure_additional_condition ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:exposure_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:exposure_vehicle ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:exposure_end_age ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:exposure_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exposure_route ], + owl:onProperty biolink:exposure_type ], biolink:NamedThing ; skos:altLabel "experimental condition", "exposure" ; @@ -14133,43 +14542,41 @@ biolink:ExposureEvent a owl:Class ; skos:exactMatch ; skos:inScheme biolink: . - a owl:Class ; - rdfs:label "molecular_modification" ; - rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - . - biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:symbol ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:symbol ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneOrGeneProductOrGeneFamily ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:GeneOrGeneProduct ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:symbol ], biolink:BiologicalEntity ; skos:broadMatch ; skos:definition "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; @@ -14180,73 +14587,79 @@ biolink:Gene a owl:Class ; skos:inScheme biolink: ; skos:narrowMatch bioschemas:gene . + a owl:Class ; + rdfs:label "molecular_modification" ; + rdfs:subClassOf biolink:CausalMechanismQualifierEnum, + ; + skos:definition "A modulation mechanism through which an effect is mediated by the modification of a target, through addition of chemical moieties such phosphate groups, ubiquitin, lipids, etc., which alter its activity or cellular behavior." . + biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:mesh_terms ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:publication_type ], + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:summary ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:pages ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:keywords ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:pages ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:authors ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:pages ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:mesh_terms ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:summary ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:keywords ], + owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:keywords ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:publication_type ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:summary ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; + owl:minCardinality 0 ; owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:onProperty biolink:summary ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:authors ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:mesh_terms ], biolink:InformationContentEntity ; - skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; + skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope." ; skos:exactMatch IAO:0000311 ; skos:inScheme biolink: ; skos:narrowMatch STY:T170, @@ -14268,8 +14681,11 @@ biolink:subject_form_or_variant_qualifier a owl:DatatypeProperty ; skos:inScheme biolink: . biolink:DirectionQualifierEnum a owl:Class ; + rdfs:label "DirectionQualifierEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration of values that qualify a change or effect by its direction, i.e., whether the referenced quantity or activity is increased (including up-regulated) or decreased (including down-regulated)." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -14278,44 +14694,44 @@ biolink:DirectionQualifierEnum a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:hgvs_nomenclature ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:hgvs_nomenclature ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], + owl:onProperty biolink:hgvs_nomenclature ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:onProperty biolink:id ], biolink:BiologicalEntity ; skos:altLabel "allele" ; skos:closeMatch , @@ -14335,6 +14751,7 @@ biolink:BiologicalEntity a owl:Class ; owl:someValuesFrom biolink:ThingWithTaxon ], biolink:NamedThing ; skos:altLabel "bioentity" ; + skos:definition "A heterogeneous substance that contains genomic material or is the product of a biological process." ; skos:inScheme biolink: ; skos:narrowMatch STY:T050, STY:T129, @@ -14344,6 +14761,7 @@ biolink:BiologicalEntity a owl:Class ; biolink:GenomicEntity a owl:Class ; rdfs:label "genomic entity" ; rdfs:subClassOf ; + skos:definition "A generically dependent continuant that carries biological sequence that is part of or derived from a genome." ; skos:inScheme biolink: ; skos:narrowMatch STY:T028, . @@ -14358,12 +14776,12 @@ biolink:AnatomicalEntity a owl:Class ; rdfs:label "anatomical entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], biolink:OrganismalEntity ; - skos:definition "A subcellular location, cell type or gross anatomical part" ; + skos:definition "A part of a cellular organism at or above the granularity of a protein complex. This is a grouping class with three concrete subclasses that should be preferred when applicable: \"biolink:Cell\" for whole cells, \"biolink:CellularComponent\" for subcellular and intracellular structures (organelles, membranes, bacterial flagella, etc.), and \"biolink:GrossAnatomcialStructure\" for multicellular parts (tissues, organs, body parts). Excludes viral and other acellular biological entities." ; skos:exactMatch STY:T017, STY:T029, STY:T030, @@ -14385,130 +14803,130 @@ biolink:AnatomicalEntity a owl:Class ; ; skos:relatedMatch SNOMEDCT:123037004 . -biolink:ChemicalEntityOrGeneOrGeneProduct a owl:Class ; - rdfs:label "chemical entity or gene or gene product" ; - rdfs:subClassOf ; - skos:definition "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; - skos:inScheme biolink: . - a owl:Class ; rdfs:label "modulation" ; rdfs:subClassOf biolink:CausalMechanismQualifierEnum, - linkml:PermissibleValue . + linkml:PermissibleValue ; + skos:definition "A causal mechanism that effects the normal functioning of a protein in some way e.g., mixed agonist/antagonist or unclear whether action is positive or negative" . -biolink:ChemicalEntity a owl:Class ; + a owl:Class ; + rdfs:label "molecular_modification" ; + rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum, + linkml:PermissibleValue . + +biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:is_toxic ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalRole ; - owl:onProperty biolink:has_chemical_role ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:chembl_black_box_warning ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:chembl_prodrug ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:chembl_availability_type ], + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:chembl_prodrug ], + owl:onProperty biolink:routes_of_delivery ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:chembl_natural_product ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:available_from ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalRole ; owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:chembl_black_box_warning ], + owl:minCardinality 0 ; + owl:onProperty biolink:chembl_prodrug ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:chembl_natural_product ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:chembl_drug_warning ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugAvailabilityEnum ; - owl:onProperty biolink:available_from ], + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:chembl_natural_product ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:chembl_drug_warning ], + owl:onProperty biolink:chembl_availability_type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:max_tolerated_dose ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:chembl_natural_product ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:available_from ], + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:allValuesFrom biolink:DrugDeliveryEnum ; owl:onProperty biolink:routes_of_delivery ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:chembl_black_box_warning ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:chembl_drug_warning ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:chembl_chirality ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:trade_name ], + owl:onProperty biolink:chembl_prodrug ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:chembl_natural_product ], + owl:onProperty biolink:chembl_black_box_warning ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:trade_name ], + owl:onProperty biolink:chembl_drug_warning ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:trade_name ], + owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:chembl_availability_type ], + owl:onProperty biolink:chembl_chirality ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:chembl_chirality ], + owl:onProperty biolink:chembl_availability_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:chembl_chirality ], + owl:onProperty biolink:chembl_drug_warning ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:max_tolerated_dose ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:chembl_availability_type ], + owl:onProperty biolink:chembl_black_box_warning ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:chembl_prodrug ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:routes_of_delivery ], + owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_toxic ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:chembl_black_box_warning ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:chembl_natural_product ], + owl:onProperty biolink:chembl_availability_type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:chembl_prodrug ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:chembl_chirality ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:chembl_drug_warning ], + owl:onProperty biolink:chembl_chirality ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], biolink:NamedThing ; skos:broadMatch STY:T167 ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; @@ -14521,14 +14939,16 @@ biolink:ChemicalEntity a owl:Class ; STY:T131, WIKIDATA:Q43460564 . - a owl:Class ; - rdfs:label "molecular_modification" ; - rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum, - linkml:PermissibleValue . +biolink:ChemicalEntityOrGeneOrGeneProduct a owl:Class ; + rdfs:label "chemical entity or gene or gene product" ; + rdfs:subClassOf ; + skos:definition "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; + skos:inScheme biolink: . biolink:ChemicalOrDrugOrTreatment a owl:Class ; rdfs:label "chemical or drug or treatment" ; rdfs:subClassOf ; + skos:definition "A mixin for entities that represent chemical substances, pharmacological agents, or therapeutic interventions." ; skos:inScheme biolink: . biolink:subject_aspect_qualifier a owl:DatatypeProperty ; @@ -14568,16 +14988,16 @@ biolink:DiseaseOrPhenotypicFeature a owl:Class ; owl:allValuesFrom biolink:GeneticInheritance ; owl:onProperty biolink:inheritance ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:inheritance ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:inheritance ], biolink:BiologicalEntity ; skos:altLabel "phenome" ; - skos:definition "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; + skos:definition "A disease or an individual phenotypic feature, grouped as a single class to accommodate source vocabularies and assertions that do not distinguish the two. Prefer the more specific subclasses disease or phenotypic feature when the distinction is known." ; skos:inScheme biolink: ; - skos:narrowMatch STY:T033 . + skos:relatedMatch STY:T033 . biolink:OntologyClass a owl:Class ; rdfs:label "ontology class" ; @@ -14591,8 +15011,11 @@ biolink:OntologyClass a owl:Class ; "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc" . biolink:GeneOrGeneProductOrChemicalEntityAspectEnum a owl:Class ; + rdfs:label "GeneOrGeneProductOrChemicalEntityAspectEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration used as a qualifier to indicate the specific aspect of a gene, gene product, or chemical entity that is affected or measured in an association. Values cover activity and abundance (expression, synthesis, degradation, stability, localization, transport), molecular interactions, and a wide range of molecular modifications such as phosphorylation, methylation, acetylation, ubiquitination, and other post-translational or chemical modifications." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -14680,340 +15103,340 @@ biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_feature_name ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_label_closure ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:supporting_text ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:negated ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationContentEntity ; - owl:onProperty biolink:has_evidence ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:maxCardinality 1 ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:elevate_to_prediction ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:object_feature_name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:update_date ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:evidence_count ], + owl:allValuesFrom biolink:Study ; + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_feature_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:retrieval_source_ids ], + owl:onProperty biolink:elevate_to_prediction ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:subject_feature_name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:p_value ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_confidence_score ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:sources ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:elevate_to_prediction ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_confidence_score ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_label_closure ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:subject_category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; owl:onProperty biolink:semmed_agreement_count ], [ a owl:Restriction ; - owl:allValuesFrom biolink:KnowledgeLevelEnum ; - owl:onProperty biolink:knowledge_level ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_feature_name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_object ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Study ; - owl:onProperty biolink:has_supporting_studies ], + owl:maxCardinality 1 ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_label_closure ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:evidence_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_closure ], + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:adjusted_p_value ], + owl:onProperty biolink:semmed_agreement_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:evidence_count ], + owl:minCardinality 0 ; + owl:onProperty biolink:sources ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:p_value ], + owl:minCardinality 0 ; + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_category ], + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:elevate_to_prediction ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:adjusted_p_value ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:KnowledgeLevelEnum ; + owl:onProperty biolink:knowledge_level ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_namespace ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_supporting_studies ], + owl:onProperty biolink:p_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:evidence_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:original_predicate ], + owl:onProperty biolink:object_closure ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_feature_name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:p_value ], + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:subject_category ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:semmed_agreement_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:agent_type ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:retrieval_source_ids ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], + owl:minCardinality 0 ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_feature_name ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence_of_type ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_confidence_score ], + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:supporting_text ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:negated ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:adjusted_p_value ], + owl:minCardinality 1 ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:update_date ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:sources ], + owl:onProperty biolink:object_feature_name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; + owl:maxCardinality 1 ; owl:onProperty biolink:elevate_to_prediction ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; + owl:minCardinality 0 ; owl:onProperty biolink:publications ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_source ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_namespace ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:negated ], + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence_of_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_namespace ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_category ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AgentTypeEnum ; - owl:onProperty biolink:agent_type ], + owl:allValuesFrom biolink:InformationContentEntity ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:semmed_agreement_count ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 0 ; owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:publications ], + owl:onProperty biolink:object_feature_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:category ], + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_namespace ], + owl:minCardinality 0 ; + owl:onProperty biolink:update_date ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:minCardinality 0 ; + owl:onProperty biolink:evidence_count ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom xsd:date ; - owl:onProperty biolink:update_date ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:timepoint ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_closure ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:adjusted_p_value ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; owl:onProperty biolink:has_confidence_score ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_category_closure ], + owl:onProperty biolink:supporting_text ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], + owl:onProperty biolink:original_object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:adjusted_p_value ], + owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:agent_type ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence_of_type ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_feature_name ], + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:supporting_text ], + owl:allValuesFrom biolink:AgentTypeEnum ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:update_date ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_category ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], + owl:maxCardinality 1 ; + owl:onProperty biolink:semmed_agreement_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_feature_name ], + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_closure ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:primary_knowledge_source ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_feature_name ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:evidence_count ], + owl:allValuesFrom xsd:date ; + owl:onProperty biolink:update_date ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:sources ], + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category_closure ], + owl:minCardinality 1 ; + owl:onProperty biolink:agent_type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:original_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_evidence_of_type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualifier ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -15025,61 +15448,61 @@ biolink:Association a owl:Class ; biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:taxon ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:equivalent_identifiers ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:equivalent_identifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:information_content ], + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:provided_by ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:information_content ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:equivalent_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:taxon ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], + owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:information_content ], + owl:onProperty biolink:synonym ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:full_name ], + owl:onProperty biolink:information_content ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:information_content ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:information_content ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:full_name ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:category ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:synonym ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:taxon ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:equivalent_identifiers ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:taxon ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:provided_by ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:full_name ], biolink:Entity ; skos:definition "a databased entity or concept/class" ; @@ -15091,8 +15514,11 @@ biolink:NamedThing a owl:Class ; skos:inScheme biolink: . biolink:CausalMechanismQualifierEnum a owl:Class ; + rdfs:label "CausalMechanismQualifierEnum" ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; + skos:definition "An enumeration used as a qualifier to specify the causal or pharmacologic mechanism by which an effect is exerted in an association (e.g., agonism, antagonism, inverse agonism, allosteric modulation, activation, inhibition, and their competitive or partial variants)." ; + skos:inScheme biolink: ; linkml:permissible_values , , , @@ -15236,93 +15662,88 @@ biolink:subject a owl:ObjectProperty ; skos:inScheme biolink: . [] a owl:Restriction ; - rdfs:subClassOf biolink:Patent ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:RelationshipQuantifier . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Patent . + owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLine ; + rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLine . + owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:subject_specialization_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_specialization_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:object_specialization_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_specialization_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_specialization_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_specialization_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . + rdfs:subClassOf biolink:CodingSequence ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CodingSequence . [] a owl:Restriction ; - rdfs:subClassOf biolink:Study ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Study . + owl:someValuesFrom biolink:GeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; + rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicExposure ; + rdfs:subClassOf biolink:PairwiseMolecularInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicExposure . + owl:someValuesFrom biolink:PairwiseMolecularInteraction . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:WebPage ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:WebPage . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Disease ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Disease . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DatasetVersion ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DatasetVersion . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenomicBackgroundExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenomicBackgroundExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DrugToGeneInteractionExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ProteinFamily ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ProteinFamily . [] a owl:Restriction ; rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; @@ -15330,968 +15751,939 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypicSex ; + rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypicSex . + owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGeneAssociation ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGeneAssociation . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Invertebrate ; + rdfs:subClassOf biolink:Exon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Invertebrate . + owl:someValuesFrom biolink:Exon . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DatasetSummary ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DatasetSummary . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Outcome . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularOrganism ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularOrganism . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; + rdfs:subClassOf biolink:ChemicalEntityToBiologicalProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . + owl:someValuesFrom biolink:ChemicalEntityToBiologicalProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseMolecularInteraction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EpigenomicEntity . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Outcome . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseMolecularInteraction . + owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Case ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin . + owl:someValuesFrom biolink:CaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; + rdfs:subClassOf biolink:SequenceVariant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SensitivityQuantifier . + owl:someValuesFrom biolink:SequenceVariant . [] a owl:Restriction ; - rdfs:subClassOf biolink:Hospitalization ; + rdfs:subClassOf biolink:ClinicalAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Hospitalization . + owl:someValuesFrom biolink:ClinicalAttribute . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . + rdfs:subClassOf biolink:ChemicalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcess ; + rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcess . + owl:someValuesFrom biolink:TranscriptionFactorBindingSite . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PathologicalAnatomicalExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ProteinIsoform ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ProteinIsoform . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SubjectOfInvestigation . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:synonym ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ] ; + owl:onProperty biolink:synonym ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrVariantQualifiersMixin . + owl:someValuesFrom biolink:GeneProductMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToParticipantAssociation ; + rdfs:subClassOf biolink:ChemicalAffectsBiologicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToParticipantAssociation . + owl:someValuesFrom biolink:ChemicalAffectsBiologicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + rdfs:subClassOf biolink:NucleicAcidEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + owl:someValuesFrom biolink:NucleicAcidEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Treatment ; + rdfs:subClassOf biolink:BioticExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Treatment . + owl:someValuesFrom biolink:BioticExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:in_taxon_label ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon_label ], + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon_label ], + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon ] ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon . + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyVariable ; + rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyVariable . + owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BookChapter ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BookChapter . + owl:someValuesFrom biolink:SequenceFeatureRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:Bacterium ; + rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Bacterium . + owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicSequenceLocalization ; + rdfs:subClassOf biolink:OrganismAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicSequenceLocalization . + owl:someValuesFrom biolink:OrganismAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:Device ; + rdfs:subClassOf biolink:StudyVariable ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Device . + owl:someValuesFrom biolink:StudyVariable . [] a owl:Restriction ; - rdfs:subClassOf biolink:Haplotype ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Haplotype . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:subject ], [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DrugToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalMixture ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalMixture . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MaterialSample ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Onset ; + rdfs:subClassOf biolink:BehavioralFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Onset . + owl:someValuesFrom biolink:BehavioralFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + rdfs:subClassOf biolink:GeneFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + owl:someValuesFrom biolink:GeneFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; + rdfs:subClassOf biolink:Device ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . + owl:someValuesFrom biolink:Device . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + rdfs:subClassOf biolink:InformationContentEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . + owl:someValuesFrom biolink:InformationContentEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalSex ; + rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalSex . + owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Behavior ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Behavior . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Zygosity ; + rdfs:subClassOf biolink:Patent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Zygosity . + owl:someValuesFrom biolink:Patent . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + rdfs:subClassOf biolink:Serial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + owl:someValuesFrom biolink:Serial . [] a owl:Restriction ; - rdfs:subClassOf biolink:SmallMolecule ; + rdfs:subClassOf biolink:OrganismToOrganismAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SmallMolecule . + owl:someValuesFrom biolink:OrganismToOrganismAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + rdfs:subClassOf biolink:EnvironmentalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + owl:someValuesFrom biolink:EnvironmentalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularComplex ; + rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularComplex . + owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugLabel ; + rdfs:subClassOf biolink:LifeStage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugLabel . + owl:someValuesFrom biolink:LifeStage . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . + rdfs:subClassOf biolink:Attribute ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Attribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:PreprintPublication ; + rdfs:subClassOf biolink:BiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PreprintPublication . + owl:someValuesFrom biolink:BiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:Snv ; + rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Snv . + owl:someValuesFrom biolink:EnvironmentalFoodContaminant . [] a owl:Restriction ; - rdfs:subClassOf biolink:AdministrativeEntity ; + rdfs:subClassOf biolink:StudyPopulation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AdministrativeEntity . + owl:someValuesFrom biolink:StudyPopulation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Protein ; + rdfs:subClassOf biolink:BiologicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Protein . + owl:someValuesFrom biolink:BiologicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularEntity ; + rdfs:subClassOf biolink:Drug ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularEntity . + owl:someValuesFrom biolink:Drug . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + rdfs:subClassOf biolink:Cohort ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + owl:someValuesFrom biolink:Cohort . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxon ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxon . + owl:someValuesFrom biolink:GeneOrGeneProductOrGeneFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProductIsoform ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProductIsoform . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:MicroRNA ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentAdverseEventAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MicroRNA . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentAdverseEventAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Gene ; + rdfs:subClassOf biolink:Procedure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Gene . + owl:someValuesFrom biolink:Procedure . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:SocioeconomicAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:SocioeconomicAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:Dataset ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Dataset . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiagnosticAid ; + rdfs:subClassOf biolink:MolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiagnosticAid . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . + owl:someValuesFrom biolink:MolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:WebPage ; + rdfs:subClassOf biolink:Agent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:WebPage . + owl:someValuesFrom biolink:Agent . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalEntity ; + rdfs:subClassOf biolink:Article ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalEntity . + owl:someValuesFrom biolink:Article . [] a owl:Restriction ; - rdfs:subClassOf biolink:LifeStage ; + rdfs:subClassOf biolink:GeneToGeneProductRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LifeStage . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene_or_gene_product ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin . + owl:someValuesFrom biolink:GeneToGeneProductRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cohort ; + rdfs:subClassOf biolink:ProteinDomain ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cohort . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineMixin . + owl:someValuesFrom biolink:ProteinDomain . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityToBiologicalProcessAssociation ; + rdfs:subClassOf biolink:GenotypeToVariantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityToBiologicalProcessAssociation . + owl:someValuesFrom biolink:GenotypeToVariantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; + rdfs:subClassOf biolink:StudyResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + owl:someValuesFrom biolink:StudyResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalIntervention ; + rdfs:subClassOf biolink:Gene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalIntervention . + owl:someValuesFrom biolink:Gene . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismAttribute ; + rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismAttribute . + owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; + rdfs:subClassOf biolink:CellularComponent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . + owl:someValuesFrom biolink:CellularComponent . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_specialization_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_specialization_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:disease_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PhysicalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysicalEntity . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SpecificityQuantifier . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Phenomenon ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Phenomenon . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:subject_specialization_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object_specialization_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:disease_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_specialization_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:disease_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_specialization_qualifier ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin . + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:EvidenceType ; + rdfs:subClassOf biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EvidenceType . + owl:someValuesFrom biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . + owl:someValuesFrom biolink:ChiSquaredAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityToChemicalEntityAssociation ; + rdfs:subClassOf biolink:SeverityValue ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityToChemicalEntityAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:JournalArticle ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:JournalArticle . + owl:someValuesFrom biolink:SeverityValue . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityToChemicalDerivationAssociation ; + rdfs:subClassOf biolink:BiologicalSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityToChemicalDerivationAssociation . + owl:someValuesFrom biolink:BiologicalSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:PlanetaryEntity ; + rdfs:subClassOf biolink:CaseToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PlanetaryEntity . + owl:someValuesFrom biolink:CaseToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PosttranslationalModification ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PosttranslationalModification . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Genome ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genome . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ContributorAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ContributorAssociation . + owl:someValuesFrom biolink:SensitivityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:Evidence ; + rdfs:subClassOf biolink:Pathway ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Evidence . + owl:someValuesFrom biolink:Pathway . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation ; + rdfs:subClassOf biolink:SequenceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation . + owl:someValuesFrom biolink:SequenceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Food ; + rdfs:subClassOf biolink:GeographicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Food . + owl:someValuesFrom biolink:GeographicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genotype ; + rdfs:subClassOf biolink:Behavior ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genotype . + owl:someValuesFrom biolink:Behavior . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:TranscriptToGeneRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:TranscriptToGeneRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcess ; + rdfs:subClassOf biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcess . + owl:someValuesFrom biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Pathway ; + rdfs:subClassOf biolink:GenotypeToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Pathway . + owl:someValuesFrom biolink:GenotypeToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation ; + rdfs:subClassOf biolink:ChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation . + owl:someValuesFrom biolink:ChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:synonym ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ] ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductMixin . + owl:someValuesFrom biolink:GeneToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneticInheritance ; + rdfs:subClassOf biolink:PreprintPublication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneticInheritance . + owl:someValuesFrom biolink:PreprintPublication . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntity ; + rdfs:subClassOf biolink:ComplexChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntity . + owl:someValuesFrom biolink:ComplexChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptionFactorBindingSite . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ActivityAndBehavior . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThing ; + rdfs:subClassOf biolink:Mammal ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThing . + owl:someValuesFrom biolink:Mammal . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; + rdfs:subClassOf biolink:GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . + owl:someValuesFrom biolink:GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToVariantAssociation ; + rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToVariantAssociation . + owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGoTermAssociation ; + rdfs:subClassOf biolink:Evidence ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGoTermAssociation . + owl:someValuesFrom biolink:Evidence . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ClinicalMeasurement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ClinicalMeasurement . [] a owl:Restriction ; - rdfs:subClassOf biolink:Book ; + rdfs:subClassOf biolink:RegulatoryRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Book . + owl:someValuesFrom biolink:RegulatoryRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExonToTranscriptRelationship ; + rdfs:subClassOf biolink:Vertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExonToTranscriptRelationship . + owl:someValuesFrom biolink:Vertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; + rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChiSquaredAnalysisResult . + owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:CommonDataElement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:CommonDataElement . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneAssociation ; + rdfs:subClassOf biolink:FoodAdditive ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneAssociation . + owl:someValuesFrom biolink:FoodAdditive . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + rdfs:subClassOf biolink:MaterialSample ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + owl:someValuesFrom biolink:MaterialSample . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToDiseaseAssociation ; + rdfs:subClassOf biolink:NamedThing ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToDiseaseAssociation . + owl:someValuesFrom biolink:NamedThing . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:PathologicalProcessExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:PathologicalProcessExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalAffectsBiologicalEntityAssociation ; + rdfs:subClassOf biolink:ExposureEvent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalAffectsBiologicalEntityAssociation . + owl:someValuesFrom biolink:ExposureEvent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Mammal ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Mammal . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivity ; + rdfs:subClassOf biolink:DrugLabel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivity . + owl:someValuesFrom biolink:DrugLabel . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation ; + rdfs:subClassOf biolink:ConceptCountAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation . + owl:someValuesFrom biolink:ConceptCountAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:ClinicalTrial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:ClinicalTrial . [] a owl:Restriction ; - rdfs:subClassOf biolink:Vertebrate ; + rdfs:subClassOf biolink:ClinicalModifier ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Vertebrate . + owl:someValuesFrom biolink:ClinicalModifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Event ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Event . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugExposure ; + rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugExposure . + owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalExposure ; + rdfs:subClassOf biolink:ReactionToParticipantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalExposure . + owl:someValuesFrom biolink:ReactionToParticipantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Publication ; + rdfs:subClassOf biolink:CaseToVariantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Publication . + owl:someValuesFrom biolink:CaseToVariantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneAssociation ; + rdfs:subClassOf biolink:CellularOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneAssociation . + owl:someValuesFrom biolink:CellularOrganism . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:CellLine ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ] ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismToOrganismAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismToOrganismAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalCourse ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalCourse . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Case ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Case . + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalTrial ; + rdfs:subClassOf biolink:BehavioralExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalTrial . + owl:someValuesFrom biolink:BehavioralExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicQuality ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicQuality . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene_or_gene_product ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneGroupingMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Attribute ; + rdfs:subClassOf biolink:GeneToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Attribute . + owl:someValuesFrom biolink:GeneToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; + rdfs:subClassOf biolink:IceesStudyResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . + owl:someValuesFrom biolink:IceesStudyResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; + rdfs:subClassOf biolink:ClinicalCourse ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . + owl:someValuesFrom biolink:ClinicalCourse . [] a owl:Restriction ; - rdfs:subClassOf biolink:Serial ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Serial . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:id ] ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass . @@ -16302,65 +16694,65 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Cell . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . + owl:someValuesFrom biolink:GeneToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:RegulatoryRegion ; + rdfs:subClassOf biolink:MacromolecularComplex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RegulatoryRegion . + owl:someValuesFrom biolink:MacromolecularComplex . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEvent ; + rdfs:subClassOf biolink:BookChapter ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEvent . + owl:someValuesFrom biolink:BookChapter . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConfidenceLevel ; + rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConfidenceLevel . + owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetDistribution ; + rdfs:subClassOf biolink:ReagentTargetedGene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetDistribution . + owl:someValuesFrom biolink:ReagentTargetedGene . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceAssociation ; + rdfs:subClassOf biolink:MolecularActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceAssociation . + owl:someValuesFrom biolink:MolecularActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; + rdfs:subClassOf biolink:GeneticInheritance ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . + owl:someValuesFrom biolink:GeneticInheritance . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ] ; @@ -16373,500 +16765,493 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:PhysiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinIsoform ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinIsoform . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneProductRelationship ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneProductRelationship . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:RetrievalSource ; + rdfs:subClassOf biolink:GeographicLocationAtTime ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RetrievalSource . + owl:someValuesFrom biolink:GeographicLocationAtTime . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:subject ] ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:GenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + rdfs:subClassOf biolink:Plant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToDiseaseAssociation . + owl:someValuesFrom biolink:Plant . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexMolecularMixture ; + rdfs:subClassOf biolink:VariantToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexMolecularMixture . + owl:someValuesFrom biolink:VariantToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptToGeneRelationship ; + rdfs:subClassOf biolink:Snv ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptToGeneRelationship . + owl:someValuesFrom biolink:Snv . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConceptCountAnalysisResult ; + rdfs:subClassOf biolink:ClinicalFinding ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConceptCountAnalysisResult . + owl:someValuesFrom biolink:ClinicalFinding . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; + rdfs:subClassOf biolink:Entity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . + owl:someValuesFrom biolink:Entity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Polypeptide ; + rdfs:subClassOf biolink:Study ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Polypeptide . + owl:someValuesFrom biolink:Study . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + rdfs:subClassOf biolink:RetrievalSource ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + owl:someValuesFrom biolink:RetrievalSource . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:disease_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:disease_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:disease_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrGeneQualifiersMixin . + owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathognomonicityQuantifier . + owl:someValuesFrom biolink:PathologicalEntityMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicQuality ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicQuality . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToVariantAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToVariantAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinFamily ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinFamily . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalProcess ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalProcess . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneProductIsoformMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SpecificityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocation ; + rdfs:subClassOf biolink:NucleosomeModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocation . + owl:someValuesFrom biolink:NucleosomeModification . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Outcome ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_percentage ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . + owl:someValuesFrom biolink:FrequencyQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:Drug ; + rdfs:subClassOf biolink:SiRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Drug . + owl:someValuesFrom biolink:SiRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; + rdfs:subClassOf biolink:NoncodingRNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . + owl:someValuesFrom biolink:NoncodingRNAProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; + rdfs:subClassOf biolink:ClinicalIntervention ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . + owl:someValuesFrom biolink:ClinicalIntervention . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeature ; + rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeature . + owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityToPathwayAssociation ; + rdfs:subClassOf biolink:AdministrativeEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityToPathwayAssociation . + owl:someValuesFrom biolink:AdministrativeEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPopulationAssociation ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPopulationAssociation . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . [] a owl:Restriction ; - rdfs:subClassOf biolink:SeverityValue ; + rdfs:subClassOf biolink:ChemicalEntityToChemicalDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SeverityValue . + owl:someValuesFrom biolink:ChemicalEntityToChemicalDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SiRNA ; + rdfs:subClassOf biolink:Onset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SiRNA . + owl:someValuesFrom biolink:Onset . [] a owl:Restriction ; - rdfs:subClassOf biolink:IceesStudyResult ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:IceesStudyResult . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:GrossAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:GrossAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocationAtTime ; + rdfs:subClassOf biolink:TaxonToTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocationAtTime . + owl:someValuesFrom biolink:TaxonToTaxonAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalRole ; + rdfs:subClassOf biolink:PlanetaryEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalRole . + owl:someValuesFrom biolink:PlanetaryEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Event ; + rdfs:subClassOf biolink:RNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Event . + owl:someValuesFrom biolink:RNAProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:FunctionalAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FunctionalAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Outcome ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentAdverseEventAssociation ; + rdfs:subClassOf biolink:AffinityMeasurement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentAdverseEventAssociation . + owl:someValuesFrom biolink:AffinityMeasurement . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicBackgroundExposure ; + rdfs:subClassOf biolink:RNAProductIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicBackgroundExposure . + owl:someValuesFrom biolink:RNAProductIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntity ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntity . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReagentTargetedGene ; + rdfs:subClassOf biolink:CellLine ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReagentTargetedGene . + owl:someValuesFrom biolink:CellLine . [] a owl:Restriction ; - rdfs:subClassOf biolink:CodingSequence ; + rdfs:subClassOf biolink:EnvironmentalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CodingSequence . + owl:someValuesFrom biolink:EnvironmentalProcess . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence . + rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EntityToDiseaseAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin . + rdfs:subClassOf biolink:Publication ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Publication . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; + rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidSequenceMotif . + owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BioticExposure ; + rdfs:subClassOf biolink:PhenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BioticExposure . + owl:someValuesFrom biolink:PhenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityPartOfAnatomicalEntityAssociation ; + rdfs:subClassOf biolink:ChemicalEntityToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityPartOfAnatomicalEntityAssociation . + owl:someValuesFrom biolink:ChemicalEntityToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleosomeModification ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleosomeModification . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessedMaterial ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessedMaterial . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProduct ; + rdfs:subClassOf biolink:GeneToGoTermAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProduct . + owl:someValuesFrom biolink:GeneToGoTermAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalExposure . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; + rdfs:subClassOf biolink:OrganismTaxon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . + owl:someValuesFrom biolink:OrganismTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; + rdfs:subClassOf biolink:DrugExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . + owl:someValuesFrom biolink:DrugExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Fungus ; + rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Fungus . + owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; + rdfs:subClassOf biolink:Protein ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneInteractionExposure . + owl:someValuesFrom biolink:Protein . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntity . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexChemicalExposure ; + rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexChemicalExposure . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Disease ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Disease . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Food ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Food . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneFamily ; + rdfs:subClassOf biolink:SocioeconomicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneFamily . + owl:someValuesFrom biolink:SocioeconomicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalMixture ; + rdfs:subClassOf biolink:MolecularEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalMixture . + owl:someValuesFrom biolink:MolecularEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:FoodAdditive ; + rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FoodAdditive . + owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularMixture ; + rdfs:subClassOf biolink:Zygosity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularMixture . + owl:someValuesFrom biolink:Zygosity . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:RelationshipQuantifier . + owl:someValuesFrom biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Activity ; + rdfs:subClassOf biolink:PhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Activity . + owl:someValuesFrom biolink:PhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidEntity ; + rdfs:subClassOf biolink:LogOddsAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidEntity . + owl:someValuesFrom biolink:LogOddsAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinDomain ; + rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinDomain . + owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalEntity ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalEntity . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityHasPartAnatomicalEntityAssociation ; + rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityHasPartAnatomicalEntityAssociation . + owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; @@ -16874,817 +17259,858 @@ biolink:subject a owl:ObjectProperty ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . + owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariant ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariant . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicSex ; + rdfs:subClassOf biolink:PopulationToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicSex . + owl:someValuesFrom biolink:PopulationToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralExposure ; + rdfs:subClassOf biolink:GeographicLocation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralExposure . + owl:someValuesFrom biolink:GeographicLocation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Case ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin . + rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; + rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . + owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Article ; + rdfs:subClassOf biolink:GenomicSequenceLocalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Article . + owl:someValuesFrom biolink:GenomicSequenceLocalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:Entity ; + rdfs:subClassOf biolink:Virus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Entity . + owl:someValuesFrom biolink:Virus . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation . + rdfs:subClassOf biolink:PosttranslationalModification ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PosttranslationalModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:Plant ; + rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Plant . + owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalModifier ; + rdfs:subClassOf biolink:Book ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalModifier . + owl:someValuesFrom biolink:Book . [] a owl:Restriction ; - rdfs:subClassOf biolink:GrossAnatomicalStructure ; + rdfs:subClassOf biolink:ClinicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GrossAnatomicalStructure . + owl:someValuesFrom biolink:ClinicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicExposure ; + rdfs:subClassOf biolink:FunctionalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicExposure . + owl:someValuesFrom biolink:FunctionalAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + rdfs:subClassOf biolink:ExonToTranscriptRelationship ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ExonToTranscriptRelationship . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BiologicalProcessOrActivity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenotypicSex ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypicSex . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Case ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Case . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:disease_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:disease_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ] ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Treatment ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Treatment . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismalEntity . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathognomonicityQuantifier . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Association ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Association . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:phenotypic_state ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:expression_site ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQualifierMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DrugToGeneAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DrugToGeneAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:expression_site ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:phenotypic_state ], + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ] ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin . + owl:someValuesFrom biolink:EntityToFeatureOrVariantQualifiersMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicAttribute ; + rdfs:subClassOf biolink:EnvironmentalFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicAttribute . + owl:someValuesFrom biolink:EnvironmentalFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyPopulation ; + rdfs:subClassOf biolink:AnatomicalEntityHasPartAnatomicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyPopulation . + owl:someValuesFrom biolink:AnatomicalEntityHasPartAnatomicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + rdfs:subClassOf biolink:Phenomenon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseAssociation . + owl:someValuesFrom biolink:Phenomenon . [] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToGeneAssociation ; + rdfs:subClassOf biolink:ChemicalEntityToChemicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToGeneAssociation . + owl:someValuesFrom biolink:ChemicalEntityToChemicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalMeasurement ; + rdfs:subClassOf biolink:Haplotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalMeasurement . + owl:someValuesFrom biolink:Haplotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralFeature ; + rdfs:subClassOf biolink:DiagnosticAid ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralFeature . + owl:someValuesFrom biolink:DiagnosticAid . [] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ComplexMolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ComplexMolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:Human ; + rdfs:subClassOf biolink:IndividualOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Human . + owl:someValuesFrom biolink:IndividualOrganism . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:JournalArticle ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:JournalArticle . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Hospitalization ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Hospitalization . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:AnatomicalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:AnatomicalEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ConfidenceLevel ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ConfidenceLevel . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity . + owl:someValuesFrom biolink:VariantToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; + rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . + owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToDiseaseAssociation ; + rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToDiseaseAssociation . + owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct . + rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ReactionToCatalystAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; + rdfs:subClassOf biolink:AnatomicalEntityPartOfAnatomicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . + owl:someValuesFrom biolink:AnatomicalEntityPartOfAnatomicalEntityAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:AccessibleDnaRegion ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AccessibleDnaRegion . - -[] a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProductOrGeneFamily . + owl:someValuesFrom biolink:GeneExpressionMixin . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon_label ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . + owl:someValuesFrom biolink:ThingWithTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation ; + rdfs:subClassOf biolink:VariantToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation . + owl:someValuesFrom biolink:VariantToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcessExposure ; + rdfs:subClassOf biolink:Genotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcessExposure . + owl:someValuesFrom biolink:Genotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; + rdfs:subClassOf biolink:EvidenceType ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceFeatureRelationship . + owl:someValuesFrom biolink:EvidenceType . [] a owl:Restriction ; - rdfs:subClassOf biolink:Transcript ; + rdfs:subClassOf biolink:CaseToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Transcript . + owl:someValuesFrom biolink:CaseToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AffinityMeasurement ; + rdfs:subClassOf biolink:Invertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AffinityMeasurement . + owl:someValuesFrom biolink:Invertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:ProcessedMaterial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:ProcessedMaterial . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntity . + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; + rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NoncodingRNAProduct . + owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:PathologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . + owl:someValuesFrom biolink:PathologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalFinding ; + rdfs:subClassOf biolink:MacromolecularMachineHasSubstrateAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalFinding . + owl:someValuesFrom biolink:MacromolecularMachineHasSubstrateAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyResult ; + rdfs:subClassOf biolink:TextMiningStudyResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyResult . + owl:someValuesFrom biolink:TextMiningStudyResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; + rdfs:subClassOf biolink:Genome ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneAssociation . + owl:someValuesFrom biolink:Genome . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSample ; + rdfs:subClassOf biolink:Fungus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSample . + owl:someValuesFrom biolink:Fungus . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; + rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . + owl:someValuesFrom biolink:EntityToFeatureOrGeneQualifiersMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:LogOddsAnalysisResult ; + rdfs:subClassOf biolink:MicroRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LogOddsAnalysisResult . + owl:someValuesFrom biolink:MicroRNA . [] a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; + rdfs:subClassOf biolink:SmallMolecule ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalStructure . + owl:someValuesFrom biolink:SmallMolecule . [] a owl:Restriction ; - rdfs:subClassOf biolink:TextMiningStudyResult ; + rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TextMiningStudyResult . + owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetSummary ; + rdfs:subClassOf biolink:PhysicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetSummary . + owl:someValuesFrom biolink:PhysicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFeature ; + rdfs:subClassOf biolink:DatasetDistribution ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFeature . + owl:someValuesFrom biolink:DatasetDistribution . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Exon ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Exon . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation . + owl:someValuesFrom biolink:GeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + rdfs:subClassOf biolink:Activity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . + owl:someValuesFrom biolink:Activity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; + rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . + owl:someValuesFrom biolink:NucleicAcidSequenceMotif . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin . + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseAssociatedWithResponseToChemicalEntityAssociation ; + rdfs:subClassOf biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseAssociatedWithResponseToChemicalEntityAssociation . + owl:someValuesFrom biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:frequency_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin . + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularComponent ; + rdfs:subClassOf biolink:Bacterium ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularComponent . + owl:someValuesFrom biolink:Bacterium . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPathwayAssociation ; + rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPathwayAssociation . + owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ContributorAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ContributorAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Virus ; + rdfs:subClassOf biolink:VariantToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Virus . + owl:someValuesFrom biolink:VariantToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; + rdfs:subClassOf biolink:Transcript ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + owl:someValuesFrom biolink:Transcript . [] a owl:Restriction ; - rdfs:subClassOf biolink:Agent ; + rdfs:subClassOf biolink:ChemicalRole ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Agent . + owl:someValuesFrom biolink:ChemicalRole . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineHasSubstrateAssociation ; + rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineHasSubstrateAssociation . + owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Dataset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Dataset . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToCatalystAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier . + owl:someValuesFrom biolink:PathologicalAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; + rdfs:subClassOf biolink:AccessibleDnaRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . + owl:someValuesFrom biolink:AccessibleDnaRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; + rdfs:subClassOf biolink:Polypeptide ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . + owl:someValuesFrom biolink:Polypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; + rdfs:subClassOf biolink:Human ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . + owl:someValuesFrom biolink:Human . [] a owl:Restriction ; - rdfs:subClassOf biolink:Procedure ; + rdfs:subClassOf biolink:DiseaseAssociatedWithResponseToChemicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Procedure . + owl:someValuesFrom biolink:DiseaseAssociatedWithResponseToChemicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; + rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . + owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:TaxonToTaxonAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TaxonToTaxonAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:onProperty biolink:qualified_predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:IndividualOrganism ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:IndividualOrganism . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetVersion ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetVersion . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CommonDataElement ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CommonDataElement . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationToPopulationAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationToPopulationAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalAttribute ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalAttribute . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Association ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Association . + owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . diff --git a/project/prefixmap/biolink-model-prefix-map.json b/project/prefixmap/biolink-model-prefix-map.json index 732629fd7..781d845c4 100644 --- a/project/prefixmap/biolink-model-prefix-map.json +++ b/project/prefixmap/biolink-model-prefix-map.json @@ -113,6 +113,7 @@ "MGI": "http://identifiers.org/mgi/", "MI": "http://purl.obolibrary.org/obo/MI_", "MIR": "http://identifiers.org/mir/", + "MOD": "http://purl.obolibrary.org/obo/MOD_", "MONDO": "http://purl.obolibrary.org/obo/MONDO_", "MP": "http://purl.obolibrary.org/obo/MP_", "MPATH": "http://purl.obolibrary.org/obo/MPATH_", @@ -196,6 +197,7 @@ "UMLS": "http://identifiers.org/umls/", "UMLSSG": "https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt", "UNII": "http://identifiers.org/unii/", + "UNIMOD": "http://identifiers.org/unimod/", "UNIPROT.ISOFORM": "http://purl.uniprot.org/isoforms/", "UO-PROPERTY": "http://purl.obolibrary.org/obo/uo#", "UPHENO": "http://purl.obolibrary.org/obo/UPHENO_", @@ -258,7 +260,6 @@ "qud": "http://qudt.org/1.1/schema/qudt#", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "regulates": "http://example.org/UNKNOWN/regulates/", "schema": "http://schema.org/", "skos": "http://www.w3.org/2004/02/skos/core#", "uspto-patent": "http://www.uspto.gov/patent/grant/v1/", diff --git a/project/prefixmap/preferred_prefixes_per_class.json b/project/prefixmap/preferred_prefixes_per_class.json index 1f07cce83..282ba5178 100644 --- a/project/prefixmap/preferred_prefixes_per_class.json +++ b/project/prefixmap/preferred_prefixes_per_class.json @@ -202,6 +202,11 @@ "prefix": "CPT", "base_uri": "https://www.ama-assn.org/practice-management/cpt/", "order": 1 + }, + { + "prefix": "MAXO", + "base_uri": "http://purl.obolibrary.org/obo/MAXO_", + "order": 2 } ] }, @@ -2620,6 +2625,21 @@ } ] }, + { + "class_name": "biolink:PosttranslationalModification", + "prefix_map": [ + { + "prefix": "MOD", + "base_uri": "http://purl.obolibrary.org/obo/MOD_", + "order": 1 + }, + { + "prefix": "UNIMOD", + "base_uri": "http://identifiers.org/unimod/", + "order": 2 + } + ] + }, { "class_name": "biolink:RNAProduct", "prefix_map": [ @@ -2627,6 +2647,11 @@ "prefix": "RNACENTRAL", "base_uri": "http://identifiers.org/rnacentral/", "order": 1 + }, + { + "prefix": "mirbase", + "base_uri": "http://identifiers.org/mirbase", + "order": 2 } ] }, @@ -2677,6 +2702,11 @@ "prefix": "WormBase", "base_uri": "https://www.wormbase.org/get?name=", "order": 3 + }, + { + "prefix": "mirbase", + "base_uri": "http://identifiers.org/mirbase", + "order": 4 } ] }, diff --git a/project/protobuf/biolink_model.proto b/project/protobuf/biolink_model.proto index eae4e0d29..1b54ff359 100644 --- a/project/protobuf/biolink_model.proto +++ b/project/protobuf/biolink_model.proto @@ -86,7 +86,7 @@ message Agent string id = 0 labelType name = 0 } -// A subcellular location, cell type or gross anatomical part +// A part of a cellular organism at or above the granularity of a protein complex. This is a grouping class with three concrete subclasses that should be preferred when applicable: "biolink:Cell" for whole cells, "biolink:CellularComponent" for subcellular and intracellular structures (organelles, membranes, bacterial flagella, etc.), and "biolink:GrossAnatomcialStructure" for multicellular parts (tissues, organs, body parts). Excludes viral and other acellular biological entities. message AnatomicalEntity { string id = 0 @@ -395,6 +395,7 @@ message Bacterium labelType inTaxonLabel = 0 repeated attribute hasAttribute = 0 } +// The internally coordinated responses (actions or inactions) of organisms (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. message Behavior { string id = 0 @@ -471,9 +472,9 @@ message BehaviorToBehavioralFeatureAssociation behavior subject = 0 behavioralFeature object = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 @@ -740,6 +741,7 @@ message BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation geneOrGeneProductOrGeneFamily object = 0 uriorcurie predicate = 0 } +// An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. message BiologicalSex { string id = 0 @@ -818,6 +820,7 @@ message Book string id = 0 repeated string type = 0 } +// A section of a book that forms a discrete unit of a larger published work and may be independently authored or cited. message BookChapter { iriType iri = 0 @@ -1032,9 +1035,9 @@ message CaseToPhenotypicFeatureAssociation boolean negated = 0 onset onsetQualifier = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 @@ -1098,6 +1101,7 @@ message CaseToVariantAssociation sequenceVariant object = 0 zygosity hasZygosity = 0 } +// An association between a gene and a disease where variation in the gene has been shown to have a causal role in the disease. message CausalGeneToDiseaseAssociation { string id = 0 @@ -1148,13 +1152,14 @@ message CausalGeneToDiseaseAssociation repeated string type = 0 repeated uriorcurie category = 0 string subjectFormOrVariantQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 string allelicRequirement = 0 uriorcurie qualifiedPredicate = 0 geneOrGeneProduct subject = 0 disease object = 0 } +// The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. message Cell { string id = 0 @@ -1175,6 +1180,7 @@ message Cell labelType inTaxonLabel = 0 repeated attribute hasAttribute = 0 } +// A cultured cell population that is genetically stable and homogeneous, sharing a common propagation history through successive passages in culture. message CellLine { string id = 0 @@ -1195,6 +1201,7 @@ message CellLine labelType inTaxonLabel = 0 repeated attribute hasAttribute = 0 } +// An association in which a cell line - typically derived from an organismal entity with a disease state - serves as a model for that disease in experimental settings. message CellLineAsAModelOfDiseaseAssociation { string id = 0 @@ -1251,9 +1258,9 @@ message CellLineAsAModelOfDiseaseAssociation repeated string anatomicalContextQualifier = 0 cellLine subject = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 } @@ -1335,6 +1342,7 @@ message CellularComponent labelType inTaxonLabel = 0 repeated attribute hasAttribute = 0 } +// An organism that contains one or more cells belonging to the cellular lineages of life (Archaea, Bacteria, or Eukaryota), whose body consists of one or more cells. Distinguished from acellular biological entities such as viruses and viroids. message CellularOrganism { string id = 0 @@ -2098,9 +2106,9 @@ message ChemicalOrDrugOrTreatmentAdverseEventAssociation uriorcurie objectSpecializationQualifier = 0 repeated string anatomicalContextQualifier = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 } @@ -2161,9 +2169,9 @@ message ChemicalOrDrugOrTreatmentSideEffectAssociation uriorcurie objectSpecializationQualifier = 0 repeated string anatomicalContextQualifier = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 } @@ -2224,9 +2232,9 @@ message ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation uriorcurie objectSpecializationQualifier = 0 repeated string anatomicalContextQualifier = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 } @@ -2356,6 +2364,7 @@ message ClinicalFinding geneticInheritance inheritance = 0 repeated clinicalAttribute hasAttribute = 0 } +// A medical procedure, treatment, or action taken by healthcare professionals to modify the course of a disease or condition. message ClinicalIntervention { string id = 0 @@ -2452,6 +2461,7 @@ message ClinicalTrial repeated diseaseOrPhenotypicFeature clinicalTrialConditions = 0 date creationDate = 0 } +// A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. message CodingSequence { string id = 0 @@ -2517,7 +2527,7 @@ message CommonDataElement string format = 0 date creationDate = 0 } -// A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. +// A complex chemical exposure is an intake of a chemical mixture, other than a drug. message ComplexChemicalExposure { iriType iri = 0 @@ -2674,6 +2684,7 @@ message ContributorAssociation agent object = 0 repeated ontologyClass qualifiers = 0 } +// An association between a gene (or gene product) and a disease for which the gene is statistically correlated with the disease rather than asserted as causal. Such associations typically derive from GWAS, co-occurrence analyses, or other statistical methods, and are annotated with scores such as a z-score or a diseases confidence score. message CorrelatedGeneToDiseaseAssociation { string id = 0 @@ -2725,7 +2736,7 @@ message CorrelatedGeneToDiseaseAssociation float zScore = 0 float diseasesConfidenceScore = 0 string subjectFormOrVariantQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 string allelicRequirement = 0 uriorcurie qualifiedPredicate = 0 @@ -2734,7 +2745,7 @@ message CorrelatedGeneToDiseaseAssociation uriorcurie predicate = 0 frequencyValue frequencyQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 disease diseaseContextQualifier = 0 } // an item that refers to a collection of data from a data source. @@ -2873,7 +2884,7 @@ message DiagnosticAid uriorcurie taxon = 0 repeated uriorcurie category = 0 } -// A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. +// A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. message Disease { string id = 0 @@ -2950,7 +2961,7 @@ message DiseaseAssociatedWithResponseToChemicalEntityAssociation chemicalEntity object = 0 uriorcurie predicate = 0 } -// Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature. +// A disease or an individual phenotypic feature, grouped as a single class to accommodate source vocabularies and assertions that do not distinguish the two. Prefer the more specific subclasses disease or phenotypic feature when the distinction is known. message DiseaseOrPhenotypicFeature { string id = 0 @@ -2972,7 +2983,7 @@ message DiseaseOrPhenotypicFeature labelType inTaxonLabel = 0 geneticInheritance inheritance = 0 } -// A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer. +// A disease or phenotypic feature state, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome,. message DiseaseOrPhenotypicFeatureExposure { iriType iri = 0 @@ -3217,9 +3228,9 @@ message DiseaseToPhenotypicFeatureAssociation double hasQuotient = 0 double hasPercentage = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 @@ -3400,6 +3411,7 @@ message DrugToGeneInteractionExposure repeated quantityValue hasQuantitativeValue = 0 repeated gene hasGeneOrGeneProduct = 0 } +// An association between a gene (or gene product) and a disease in which the gene is classified by its druggability (e.g., via the IDG/Pharos target development-level tiers). message DruggableGeneToDiseaseAssociation { string id = 0 @@ -3461,9 +3473,10 @@ message DruggableGeneToDiseaseAssociation geneToDiseasePredicateEnum predicate = 0 frequencyValue frequencyQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 disease diseaseContextQualifier = 0 } +// An association between any entity and a disease, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases. message EntityToDiseaseAssociation { string id = 0 @@ -3520,6 +3533,7 @@ message EntityToDiseaseAssociation repeated string fDARegulatoryApprovals = 0 integer numberOfCases = 0 } +// An association between any entity and a phenotypic feature, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases. message EntityToPhenotypicFeatureAssociation { string id = 0 @@ -3604,6 +3618,7 @@ message EnvironmentalExposure string exposureAdditionalCondition = 0 string id = 0 } +// A system or entity in the natural environment that has the disposition to environ one or more material entities. message EnvironmentalFeature { string id = 0 @@ -3622,6 +3637,7 @@ message EnvironmentalFeature uriorcurie taxon = 0 repeated uriorcurie category = 0 } +// Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate foodstuffs during their production, transportation or storage. message EnvironmentalFoodContaminant { string id = 0 @@ -3652,6 +3668,7 @@ message EnvironmentalFoodContaminant string chemblChirality = 0 string chemblDrugWarning = 0 } +// A process that occurs within or involves the components of an environmental system. message EnvironmentalProcess { string id = 0 @@ -3941,9 +3958,9 @@ message ExposureEventToPhenotypicFeatureAssociation repeated uriorcurie category = 0 exposureEvent subject = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 @@ -3953,7 +3970,7 @@ message ExposureEventToPhenotypicFeatureAssociation double hasQuotient = 0 double hasPercentage = 0 } -// A substance consumed by a living organism as a source of nutrition +// A substance of plant, animal, or artificial origin consumed by a living organism to provide essential nutrients, energy, and support growth and the processes of life, or to satisfy other health needs or provide a social or organoleptic experience. message Food { string id = 0 @@ -3987,6 +4004,7 @@ message Food approvalStatusEnum highestFDAApprovalStatus = 0 approvalStatusEnum drugRegulatoryStatusWorldWide = 0 } +// Any substance which is added to food to preserve or enhance its flavour and/or appearance. message FoodAdditive { string id = 0 @@ -4070,7 +4088,6 @@ message FunctionalAssociation macromolecularMachineMixin subject = 0 ontologyClass object = 0 } -// A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds). message Fungus { string id = 0 @@ -4179,10 +4196,11 @@ message GeneAffectsChemicalAssociation repeated anatomicalEntity anatomicalContextQualifier = 0 uriorcurie qualifiedPredicate = 0 organismTaxon speciesContextQualifier = 0 - geneOrGeneProduct subject = 0 + chemicalEntityOrGeneOrGeneProduct subject = 0 uriorcurie predicate = 0 chemicalEntity object = 0 } +// An association in which a gene (e.g., a model-organism ortholog of a known disease gene) serves as a model of a human disease - for example, because mutants of the gene recapitulate core features of the disease. message GeneAsAModelOfDiseaseAssociation { string id = 0 @@ -4243,7 +4261,7 @@ message GeneAsAModelOfDiseaseAssociation geneOrGeneProduct subject = 0 frequencyValue frequencyQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 disease diseaseContextQualifier = 0 } // any grouping of multiple genes or gene products related by common descent @@ -4317,10 +4335,11 @@ message GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation integer semmedAgreementCount = 0 repeated string type = 0 repeated uriorcurie category = 0 - gene subject = 0 - geneFamily object = 0 + geneFamily subject = 0 + geneOrGeneProduct object = 0 uriorcurie predicate = 0 } +// A gene-to-disease association that is asserted on the grounds that the gene harbours a sequence variant that contributes to the disease. Qualifies the gene with the form or variant that underlies the contribution. message GeneHasVariantThatContributesToDiseaseAssociation { string id = 0 @@ -4539,10 +4558,11 @@ message GeneRegulatesGeneAssociation directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 organismTaxon speciesContextQualifier = 0 - geneOrGeneProduct subject = 0 + chemicalEntityOrGeneOrGeneProduct subject = 0 uriorcurie predicate = 0 - geneOrGeneProduct object = 0 + chemicalEntityOrGeneOrGeneProduct object = 0 } +// An association between a gene or gene product and a disease, where variation in the gene is correlated with the disease. message GeneToDiseaseAssociation { string id = 0 @@ -4874,6 +4894,7 @@ message GeneToGeneProductRelationship geneProductMixin object = 0 uriorcurie predicate = 0 } +// A functional association between a gene (or gene product or macromolecular complex) and a Gene Ontology (GO) term describing the molecular function, biological process, or cellular component in which it participates. message GeneToGoTermAssociation { string id = 0 @@ -4979,6 +5000,7 @@ message GeneToPathwayAssociation geneOrGeneProduct subject = 0 pathway object = 0 } +// An association between a gene or gene product and a phenotypic feature, where variation in the gene is correlated with the phenotypic feature. message GeneToPhenotypicFeatureAssociation { string id = 0 @@ -5036,7 +5058,7 @@ message GeneToPhenotypicFeatureAssociation geneToPhenotypicFeaturePredicateEnum predicate = 0 frequencyValue frequencyQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 biologicalSex sexQualifier = 0 @@ -5045,7 +5067,7 @@ message GeneToPhenotypicFeatureAssociation double hasQuotient = 0 double hasPercentage = 0 } -// The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc. +// The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next. message GeneticInheritance { string id = 0 @@ -5201,6 +5223,7 @@ message Genotype zygosity hasZygosity = 0 biologicalSequence hasBiologicalSequence = 0 } +// An association in which a genotype serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it. message GenotypeAsAModelOfDiseaseAssociation { string id = 0 @@ -5252,14 +5275,15 @@ message GenotypeAsAModelOfDiseaseAssociation uriorcurie predicate = 0 namedThing object = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 genotype subject = 0 } +// An association between a genotype and a disease, in which the genotype (typically a combination of alleles at one or more loci) is linked to the disease state. message GenotypeToDiseaseAssociation { string id = 0 @@ -5312,9 +5336,9 @@ message GenotypeToDiseaseAssociation uriorcurie predicate = 0 namedThing object = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 @@ -5478,9 +5502,9 @@ message GenotypeToPhenotypicFeatureAssociation uriorcurie predicate = 0 genotype subject = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 @@ -5636,6 +5660,7 @@ message GeographicLocationAtTime float longitude = 0 timeType timepoint = 0 } +// An anatomical structure that has more than one cell as a part. message GrossAnatomicalStructure { string id = 0 @@ -5678,6 +5703,7 @@ message Haplotype labelType inTaxonLabel = 0 biologicalSequence hasBiologicalSequence = 0 } +// The admission and care of a patient in a hospital for observation, diagnosis, or treatment. message Hospitalization { string id = 0 @@ -5696,7 +5722,6 @@ message Hospitalization uriorcurie taxon = 0 repeated uriorcurie category = 0 } -// A member of the the species Homo sapiens. message Human { string id = 0 @@ -5744,7 +5769,7 @@ message IceesStudyResult float logOddsRatio = 0 repeated float logOddsRatio95Ci = 0 } -// An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576 +// An instance of an organism. For example, Charles Darwin, my pet cat. message IndividualOrganism { string id = 0 @@ -5818,7 +5843,6 @@ message InformationContentEntityToNamedThingAssociation namedThing object = 0 uriorcurie predicate = 0 } -// An animal lacking a vertebral column. This group consists of 98% of all animal species. message Invertebrate { string id = 0 @@ -5872,7 +5896,7 @@ message JournalArticle string volume = 0 string issue = 0 } -// A knowledge graph represented in KGX format +// A container representing a knowledge graph serialized in KGX (Knowledge Graph Exchange) format. A KnowledgeGraph aggregates a collection of nodes (entities) and edges (relationships between entities) conforming to the KGX specification, enabling interoperable exchange of biomedical knowledge graphs across tools and systems in the Biolink ecosystem. message KnowledgeGraph { repeated entity nodes = 0 @@ -6154,7 +6178,6 @@ message MacromolecularMachineToMolecularActivityAssociation molecularActivity object = 0 organismTaxon speciesContextQualifier = 0 } -// A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex message Mammal { string id = 0 @@ -6304,6 +6327,7 @@ message MaterialSampleToDiseaseOrPhenotypicFeatureAssociation uriorcurie objectSpecializationQualifier = 0 repeated string anatomicalContextQualifier = 0 } +// A small (~22 nucleotide) RNA molecule that is the endogenous transcript of a miRNA gene. Produced from precursor molecules that form hairpin structures, which are processed (typically via the Dicer pathway) to yield a single miRNA molecule. miRNAs function by triggering cleavage of target molecules or acting as translational repressors. message MicroRNA { string id = 0 @@ -6592,6 +6616,7 @@ message NamedThing uriorcurie taxon = 0 repeated uriorcurie category = 0 } +// An association in which the subject entity is linked to the likelihood of the object entity occurring, manifesting, or being observed. Subject and object may each be qualified by aspect and context, and the association may be further qualified by a population context. message NamedThingAssociatedWithLikelihoodOfNamedThingAssociation { string id = 0 @@ -6641,14 +6666,15 @@ message NamedThingAssociatedWithLikelihoodOfNamedThingAssociation repeated string type = 0 repeated uriorcurie category = 0 namedThing subject = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 ontologyClass subjectContextQualifier = 0 uriorcurie predicate = 0 namedThing object = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 ontologyClass objectContextQualifier = 0 populationOfIndividualOrganisms populationContextQualifier = 0 } +// An RNA transcript that does not encode for a protein rather the RNA molecule is the functional gene product. message NoncodingRNAProduct { string id = 0 @@ -6704,7 +6730,7 @@ message NucleicAcidEntity repeated organismTaxon inTaxon = 0 labelType inTaxonLabel = 0 } -// A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences. +// A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. consensus sequences. message NucleicAcidSequenceMotif { string id = 0 @@ -6725,7 +6751,7 @@ message NucleicAcidSequenceMotif repeated organismTaxon inTaxon = 0 labelType inTaxonLabel = 0 } -// A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A. +// A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. message NucleosomeModification { string id = 0 @@ -6937,6 +6963,7 @@ message OrganismTaxonToOrganismTaxonSpecialization organismTaxon object = 0 uriorcurie predicate = 0 } +// An association between two individual organisms (e.g., symbiosis, parasitism, predation, or other inter-organism relationships). message OrganismToOrganismAssociation { string id = 0 @@ -6989,6 +7016,7 @@ message OrganismToOrganismAssociation individualOrganism subject = 0 individualOrganism object = 0 } +// An association in which an organismal entity (e.g., a strain or breed) serves as a model of a disease, either because it has a natural predisposition to the disease or was bred or engineered specifically to recapitulate it. message OrganismalEntityAsAModelOfDiseaseAssociation { string id = 0 @@ -7041,9 +7069,9 @@ message OrganismalEntityAsAModelOfDiseaseAssociation repeated uriorcurie category = 0 organismalEntity subject = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 @@ -7184,7 +7212,7 @@ message Patent string id = 0 labelType name = 0 } -// An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome. +// An abnormal anatomical structure, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome. message PathologicalAnatomicalExposure { iriType iri = 0 @@ -7257,7 +7285,7 @@ message PathologicalProcess repeated namedThing hasOutput = 0 repeated physicalEntity enabledBy = 0 } -// A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease. +// A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome. message PathologicalProcessExposure { iriType iri = 0 @@ -7285,6 +7313,7 @@ message PathologicalProcessExposure string exposureAdditionalCondition = 0 string id = 0 } +// A hierarchical ordering of connected molecular reactions (steps) that represent a specific biological process, such as signaling or metabolism. message Pathway { string id = 0 @@ -7327,7 +7356,7 @@ message Phenomenon uriorcurie taxon = 0 repeated uriorcurie category = 0 } -// A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment. +// A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual often resulting from the interaction of its genotype with its molecular and physical environment. message PhenotypicFeature { string id = 0 @@ -7349,6 +7378,7 @@ message PhenotypicFeature labelType inTaxonLabel = 0 geneticInheritance inheritance = 0 } +// An association between a phenotypic feature (sign or symptom) and a disease, where the phenotypic feature is a manifestation or clinical indicator of the disease. message PhenotypicFeatureToDiseaseAssociation { string id = 0 @@ -7401,9 +7431,9 @@ message PhenotypicFeatureToDiseaseAssociation repeated uriorcurie category = 0 uriorcurie predicate = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 @@ -7466,9 +7496,9 @@ message PhenotypicFeatureToPhenotypicFeatureAssociation repeated string type = 0 repeated uriorcurie category = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 biologicalSex sexQualifier = 0 @@ -7478,7 +7508,7 @@ message PhenotypicFeatureToPhenotypicFeatureAssociation double hasPercentage = 0 disease diseaseContextQualifier = 0 } -// A property of a phenotype +// A characteristic of a phenotype (e.g., weight, size, shape, color) that can be observed, measured, or compared across organisms or conditions. message PhenotypicQuality { string id = 0 @@ -7541,6 +7571,7 @@ message PhysicalEntity uriorcurie taxon = 0 repeated uriorcurie category = 0 } +// A biological or chemical function within a living organism. message PhysiologicalProcess { string id = 0 @@ -7698,7 +7729,7 @@ message PopulationToPopulationAssociation populationOfIndividualOrganisms object = 0 uriorcurie predicate = 0 } -// A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination. +// A chemical modification of a polypeptide or protein that occurs after translation, altering its structure, activity, localization, or interactions. message PosttranslationalModification { string id = 0 @@ -7723,7 +7754,7 @@ message PosttranslationalModification message PredicateMapping { string mappedPredicate = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 string subjectFormOrVariantQualifier = 0 string subjectPartQualifier = 0 @@ -7731,7 +7762,7 @@ message PredicateMapping string subjectContextQualifier = 0 uriorcurie predicate = 0 uriorcurie qualifiedPredicate = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 string objectFormOrVariantQualifier = 0 string objectPartQualifier = 0 @@ -7900,7 +7931,7 @@ message Protein repeated organismTaxon inTaxon = 0 labelType inTaxonLabel = 0 } -// A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain. +// A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. message ProteinDomain { string id = 0 @@ -7922,6 +7953,7 @@ message ProteinDomain labelType inTaxonLabel = 0 repeated gene hasGeneOrGeneProduct = 0 } +// A set of proteins coding for diverse functions which, by virtue of their high degree of sequence similarity, are believed to have evolved from a single ancestral gene. message ProteinFamily { string id = 0 @@ -7943,7 +7975,7 @@ message ProteinFamily labelType inTaxonLabel = 0 repeated gene hasGeneOrGeneProduct = 0 } -// Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ +// Represents a protein that is a specific isoform of the canonical or reference protein. message ProteinIsoform { string id = 0 @@ -7964,7 +7996,7 @@ message ProteinIsoform repeated organismTaxon inTaxon = 0 labelType inTaxonLabel = 0 } -// Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). +// Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope. message Publication { iriType iri = 0 @@ -7999,6 +8031,7 @@ message QuantityValue unit hasUnit = 0 double hasNumericValue = 0 } +// A specialization of reaction-to-participant association in which the participant is a gene or gene product (e.g., an enzyme) that catalyses the reaction. message ReactionToCatalystAssociation { string id = 0 @@ -8055,6 +8088,7 @@ message ReactionToCatalystAssociation molecularEntity subject = 0 geneOrGeneProduct object = 0 } +// An association between a biochemical reaction and a participating molecular entity, qualified by the stoichiometry, the side (reactant vs. product) on which the participant appears, and the direction of the reaction. message ReactionToParticipantAssociation { string id = 0 @@ -8206,6 +8240,7 @@ message RetrievalSource repeated uriorcurie sourceRecordUrls = 0 repeated uriorcurie xref = 0 } +// High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds typically synthesized by a DNA- or RNA-dependent RNA polymerase that constitutes the product of a gene. Distinct in emphasis from `biolink:Transcript`, which denotes the informational output of transcription at the gene-model level rather than the chemical species itself. message RNAProduct { string id = 0 @@ -8530,7 +8565,7 @@ message SocioeconomicAttribute namedThing hasQualitativeValue = 0 iriType iri = 0 } -// A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty). +// A socioeconomic exposure is a factor relating to social and financial status of an affected individual. message SocioeconomicExposure { iriType iri = 0 @@ -8622,6 +8657,7 @@ message StudyVariable string format = 0 date creationDate = 0 } +// An association between two organism taxa, capturing ecological or evolutionary relationships between the taxa (e.g., a host-pathogen relationship or shared habitat). message TaxonToTaxonAssociation { string id = 0 @@ -8832,6 +8868,7 @@ message Treatment repeated device hasDevice = 0 repeated procedure hasProcedure = 0 } +// An association in which a sequence variant serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it. message VariantAsAModelOfDiseaseAssociation { string id = 0 @@ -8883,14 +8920,15 @@ message VariantAsAModelOfDiseaseAssociation uriorcurie predicate = 0 namedThing object = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 sequenceVariant subject = 0 } +// An association between a sequence variant and a disease, in which the allele state of the variant is linked to the disease state. message VariantToDiseaseAssociation { string id = 0 @@ -8943,9 +8981,9 @@ message VariantToDiseaseAssociation uriorcurie predicate = 0 namedThing object = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 @@ -9060,6 +9098,7 @@ message VariantToGeneExpressionAssociation lifeStage stageQualifier = 0 diseaseOrPhenotypicFeature phenotypicState = 0 } +// An association between a sequence variant and a phenotypic feature, in which the allele state of the variant is linked to the manifestation of the phenotype. message VariantToPhenotypicFeatureAssociation { string id = 0 @@ -9112,9 +9151,9 @@ message VariantToPhenotypicFeatureAssociation repeated uriorcurie category = 0 sequenceVariant subject = 0 frequencyValue frequencyQualifier = 0 - string subjectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 directionQualifierEnum subjectDirectionQualifier = 0 - string objectAspectQualifier = 0 + geneOrGeneProductOrChemicalEntityAspectEnum objectAspectQualifier = 0 directionQualifierEnum objectDirectionQualifier = 0 uriorcurie qualifiedPredicate = 0 disease diseaseContextQualifier = 0 @@ -9182,7 +9221,6 @@ message VariantToPopulationAssociation double hasPercentage = 0 frequencyValue frequencyQualifier = 0 } -// A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column. message Vertebrate { string id = 0 @@ -9253,6 +9291,7 @@ message WebPage string id = 0 labelType name = 0 } +// An allelic state describing the degree of similarity between features at a single locus, specifically whether alleles at the same location on paired chromosomes are identical or different. message Zygosity { string id = 0 diff --git a/project/shacl/biolink_model.shacl.ttl b/project/shacl/biolink_model.shacl.ttl index f8708c219..8ea541338 100644 --- a/project/shacl/biolink_model.shacl.ttl +++ b/project/shacl/biolink_model.shacl.ttl @@ -7,66 +7,56 @@ @prefix xsd: . biolink:AccessibleDnaRegion a sh:NodeShape ; + rdfs:comment "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:closed true ; - sh:description "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 12 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -80,61 +70,65 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:order 11 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:information_content ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:taxon ], + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:equivalent_identifiers ] ; sh:targetClass biolink:AccessibleDnaRegion . biolink:Activity a sh:NodeShape ; + rdfs:comment "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; sh:closed true ; - sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; - sh:ignoredProperties ( biolink:clinical_trial_intervention_model biolink:clinical_trial_overall_status biolink:clinical_trial_age_range biolink:clinical_trial_conditions biolink:clinical_trial_start_date biolink:clinical_trial_brief_title biolink:clinical_trial_phase rdf:type biolink:creation_date biolink:clinical_trial_interventions biolink:clinical_trial_age_stage biolink:clinical_trial_enrollment_type biolink:has_study_results biolink:clinical_trial_tested_intervention biolink:clinical_trial_primary_purpose biolink:clinical_trial_enrollment ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:ignoredProperties ( biolink:clinical_trial_phase biolink:has_study_results biolink:creation_date biolink:clinical_trial_enrollment biolink:clinical_trial_intervention_model biolink:clinical_trial_overall_status biolink:clinical_trial_enrollment_type biolink:clinical_trial_primary_purpose biolink:clinical_trial_age_range biolink:clinical_trial_conditions biolink:clinical_trial_interventions rdf:type biolink:clinical_trial_start_date biolink:clinical_trial_brief_title biolink:clinical_trial_age_stage biolink:clinical_trial_tested_intervention ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:information_content ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -142,11 +136,22 @@ biolink:Activity a sh:NodeShape ; sh:order 11 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -154,36 +159,33 @@ biolink:Activity a sh:NodeShape ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -191,229 +193,233 @@ biolink:Activity a sh:NodeShape ; sh:order 2 ; sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ] ; + sh:order 10 ; + sh:path rdf:type ] ; sh:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; + rdfs:comment "Activity or behavior of any independent integral living, organization or mechanical actor in the world" ; sh:closed false ; - sh:description "Activity or behavior of any independent integral living, organization or mechanical actor in the world" ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:ActivityAndBehavior . biolink:AdministrativeEntity a sh:NodeShape ; + rdfs:comment "An entity that is the byproduct of an administrative process." ; sh:closed false ; - sh:ignoredProperties ( rdf:type biolink:address biolink:affiliation ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:ignoredProperties ( rdf:type biolink:affiliation biolink:address ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ] ; + sh:order 5 ; + sh:path biolink:information_content ] ; sh:targetClass biolink:AdministrativeEntity . biolink:AnatomicalEntityHasPartAnatomicalEntityAssociation a sh:NodeShape ; + rdfs:comment "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood, that is, the subject is has the object entity as a part (the expected predicate is \"biolink:has_part\" or suitable predicate slots inheriting from it, i.e., \"biolink:has_plasma_membrane_part\", \"biolink:has_variant_part\", etc.). This includes relationships between cells and cellular components, between issues and cells, whole organisms and tissues." ; sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood, that is, the subject is has the object entity as a part (the expected predicate is \"biolink:has_part\" or suitable predicate slots inheriting from it, i.e., \"biolink:has_plasma_membrane_part\", \"biolink:has_variant_part\", etc.). This includes relationships between cells and cellular components, between issues and cells, whole organisms and tissues." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the whole" ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -421,238 +427,248 @@ biolink:AnatomicalEntityHasPartAnatomicalEntityAssociation a sh:NodeShape ; sh:order 33 ; sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 43 ; + sh:path biolink:category ], [ sh:class biolink:AnatomicalEntity ; - sh:description "the part" ; + sh:description "the whole" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:has_active_ingredient biolink:has_excipient biolink:has_food_component biolink:has_nutrient biolink:has_part biolink:has_plasma_membrane_part biolink:has_variant_part ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the part" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ] ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ] ; sh:targetClass biolink:AnatomicalEntityHasPartAnatomicalEntityAssociation . biolink:AnatomicalEntityPartOfAnatomicalEntityAssociation a sh:NodeShape ; + rdfs:comment "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood, that is, the subject is a part of the object entity (the expected predicate is \"biolink:part_of\" or suitable predicate slots inheriting from it, i.e., \"biolink:plasma_membrane_part_of\", \"biolink:variant_part_of\", etc.). This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms." ; sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood, that is, the subject is a part of the object entity (the expected predicate is \"biolink:part_of\" or suitable predicate slots inheriting from it, i.e., \"biolink:plasma_membrane_part_of\", \"biolink:variant_part_of\", etc.). This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:food_component_of biolink:is_active_ingredient_of biolink:is_excipient_of biolink:nutrient_of biolink:part_of biolink:plasma_membrane_part_of biolink:variant_part_of ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:class biolink:AnatomicalEntity ; sh:description "the part" ; sh:maxCount 1 ; @@ -660,124 +676,157 @@ biolink:AnatomicalEntityPartOfAnatomicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:class biolink:AnatomicalEntity ; sh:description "the whole" ; sh:maxCount 1 ; @@ -785,229 +834,233 @@ biolink:AnatomicalEntityPartOfAnatomicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 39 ; + sh:path biolink:evidence_count ] ; + sh:targetClass biolink:AnatomicalEntityPartOfAnatomicalEntityAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; + rdfs:comment "An abstract parent class for associations between two anatomical entities, such as part-of, develops-from, or other mereological and ontogenic relationships." ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:update_date ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:AnatomicalEntityPartOfAnatomicalEntityAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -1015,247 +1068,193 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 44 ; + sh:path rdf:type ], [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:evidence_count ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ] ; + sh:path biolink:object_feature_name ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; + rdfs:comment "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:property [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:supporting_text ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -1263,70 +1262,64 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at a later time" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; @@ -1338,324 +1331,351 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; + sh:description "the structure at an earlier time" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:develops_from ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ] ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . biolink:Annotation a sh:NodeShape ; + rdfs:comment "Biolink Model root class for entity annotations." ; sh:closed false ; - sh:description "Biolink Model root class for entity annotations." ; - sh:ignoredProperties ( biolink:has_unit rdf:type biolink:has_numeric_value ) ; + sh:ignoredProperties ( rdf:type biolink:has_unit biolink:has_numeric_value ) ; sh:targetClass biolink:Annotation . biolink:Article a sh:NodeShape ; + rdfs:comment "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; sh:closed true ; - sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:property [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:information_content ], + sh:order 3 ; + sh:path biolink:issue ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:volume ], + [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:issue ], + sh:order 23 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path dct:type ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], + sh:order 11 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:volume ], + sh:order 5 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:license ], + sh:order 13 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:summary ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:category ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], + sh:order 25 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:keywords ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; + sh:order 21 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path rdf:type ], + sh:order 28 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:keywords ], + sh:order 17 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:rights ], + sh:order 19 ; + sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:synonym ] ; + sh:order 16 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:summary ] ; sh:targetClass biolink:Article . biolink:Bacterium a sh:NodeShape ; + rdfs:comment "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; sh:closed true ; - sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -1668,214 +1688,131 @@ biolink:Bacterium a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ] ; sh:targetClass biolink:Bacterium . biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; + rdfs:comment "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:closed true ; - sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 55 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 53 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:class biolink:Behavior ; + sh:description "behavior that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 59 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:has_total ], - [ sh:class biolink:BehavioralFeature ; - sh:description "behavioral feature that is the object of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 58 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 57 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], + sh:order 52 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], + sh:order 30 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 49 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -1883,17 +1820,17 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:order 11 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 60 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; @@ -1901,389 +1838,440 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:order 41 ; sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path rdfs:label ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 42 ; + sh:path biolink:id ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 56 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:order 21 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], + sh:order 47 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], + sh:order 45 ; + sh:path rdf:type ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path biolink:has_count ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:BehavioralFeature ; + sh:description "behavioral feature that is the object of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 48 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 59 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 57 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:supporting_text ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 60 ; - sh:path biolink:frequency_qualifier ], + sh:order 58 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:has_confidence_score ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 54 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 56 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 55 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; - sh:path biolink:update_date ] ; + sh:path biolink:update_date ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . biolink:BehavioralExposure a sh:NodeShape ; + rdfs:comment "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:closed true ; - sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 2 ; + sh:path biolink:exposure_vehicle ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:taxon ], + sh:order 21 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:exposure_type ], + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; + sh:order 19 ; + sh:path rdf:type ], + [ sh:datatype xsd:integer ; + sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:exposure_route ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 4 ; + sh:path biolink:exposure_start_age ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:deprecated ], + sh:order 15 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:exposure_magnitude ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Route of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], + sh:order 3 ; + sh:path biolink:exposure_route ], [ sh:datatype xsd:integer ; sh:description "Ending stage of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:exposure_end_age ], - [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:exposure_additional_condition ], + sh:order 23 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 20 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "Type of an exposure event." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:exposure_vehicle ], - [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; + sh:order 8 ; + sh:path biolink:exposure_additional_condition ], + [ sh:datatype xsd:string ; + sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:exposure_duration ], + sh:order 1 ; + sh:path biolink:exposure_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], + sh:order 17 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ] ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:exposure_duration ] ; sh:targetClass biolink:BehavioralExposure . biolink:BehavioralOutcome a sh:NodeShape ; + rdfs:comment "An outcome resulting from an exposure event which is the manifestation of human behavior." ; sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of human behavior." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:BehavioralOutcome . biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation a sh:NodeShape ; + rdfs:comment "An association between a biological process or activity and an anatomical entity." ; sh:closed true ; - sh:description "An association between a biological process or activity and an anatomical entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -2291,40 +2279,34 @@ biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation a sh:NodeShape sh:order 48 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:BiologicalProcessOrActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -2335,30 +2317,48 @@ biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation a sh:NodeShape sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:BiologicalProcessOrActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:class biolink:AnatomicalEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -2366,118 +2366,77 @@ biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation a sh:NodeShape sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:supporting_text ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -2485,129 +2444,125 @@ biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation a sh:NodeShape sh:order 18 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ] ; - sh:targetClass biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation . - -biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Classification relationship between biological processes or activities (e.g. coupling of two molecular activities; assignment of molecular activity to a pathway; implicating a pathway in a biological process; etc.)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:BiologicalProcessOrActivity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path biolink:sources ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ] ; + sh:targetClass biolink:BiologicalProcessOrActivityToAnatomicalEntityAssociation . + +biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation a sh:NodeShape ; + rdfs:comment "Classification relationship between biological processes or activities (e.g. coupling of two molecular activities; assignment of molecular activity to a pathway; implicating a pathway in a biological process; etc.)" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; @@ -2615,61 +2570,27 @@ biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation a sh sh:order 38 ; sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -2677,366 +2598,264 @@ biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation a sh sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:BiologicalProcessOrActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:anyURI ; - sh:description "One biological processes or activities is a subclass of another." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:supporting_text ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:evidence_count ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation . - -biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Relationship between a biological processor activity (e.g. molecular activity, biological process or pathway) to gene or gene product or gene family." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "One biological processes or activities is a subclass of another." ; + sh:in ( biolink:subclass_of ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:BiologicalProcessOrActivity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:BiologicalProcessOrActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Relationship in which a biological process has the participation of a gene or gene product or gene family in a (e.g., pathway has participant gene product)." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:BiologicalProcessOrActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:sources ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ] ; + sh:targetClass biolink:BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation . + +biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation a sh:NodeShape ; + rdfs:comment "Relationship between a biological processor activity (e.g. molecular activity, biological process or pathway) to gene or gene product or gene family." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 41 ; + sh:path biolink:id ], [ sh:class biolink:GeneOrGeneProductOrGeneFamily ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -3044,6 +2863,12 @@ biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation a sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -3051,10 +2876,33 @@ biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation a sh:order 16 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; @@ -3062,10 +2910,35 @@ biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation a sh:order 20 ; sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -3073,315 +2946,470 @@ biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation a sh:order 17 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation . - -biolink:BioticExposure a sh:NodeShape ; - sh:closed true ; - sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:exposure_type ], + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:taxon ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 45 ; sh:path rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "Relationship in which a biological process has the participation of a gene or gene product or gene family in a (e.g., pathway has participant gene product)." ; + sh:in ( biolink:actively_involves biolink:can_be_carried_out_by biolink:consumes biolink:enabled_by biolink:has_catalyst biolink:has_input biolink:has_output biolink:has_participant biolink:has_substrate ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:BiologicalProcessOrActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:exposure_duration ], - [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:exposure_magnitude ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 36 ; + sh:path biolink:update_date ] ; + sh:targetClass biolink:BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation . + +biolink:BioticExposure a sh:NodeShape ; + rdfs:comment "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:order 15 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], + sh:order 6 ; + sh:path biolink:exposure_duration ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "Route of exposure." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:exposure_route ], + [ sh:datatype xsd:string ; + sh:description "Type of exposure" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:exposure_type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 21 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:exposure_vehicle ], [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:exposure_route ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:exposure_additional_condition ], + sh:order 16 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Type of an exposure event." ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:exposure_vehicle ], + sh:order 5 ; + sh:path biolink:exposure_end_age ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Additional conditions impacting an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:exposure_additional_condition ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:category ], [ sh:datatype xsd:integer ; sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_end_age ] ; + sh:order 20 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:exposure_magnitude ] ; sh:targetClass biolink:BioticExposure . biolink:Book a sh:NodeShape ; + rdfs:comment "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:closed true ; - sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 21 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 18 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 22 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path dct:type ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "Books should have industry-standard identifier such as from ISBN." ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:description "Should generally be set to an ontology class defined term for 'book'." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; + sh:description "Books should have industry-standard identifier such as from ISBN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ] ; + sh:order 17 ; + sh:path biolink:id ] ; sh:targetClass biolink:Book . biolink:BookChapter a sh:NodeShape ; + rdfs:comment "A section of a book that forms a discrete unit of a larger published work and may be independently authored or cited." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:keywords ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:mesh_terms ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "chapter of a book" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:chapter ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -3389,72 +3417,44 @@ biolink:BookChapter a sh:NodeShape ; sh:order 19 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; + sh:order 23 ; + sh:path rdf:type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:format ], + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:volume ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:summary ], + sh:order 14 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:license ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:information_content ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:rights ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:deprecated ], + sh:order 25 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -3466,365 +3466,395 @@ biolink:BookChapter a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:license ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:volume ], + sh:order 9 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "chapter of a book" ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:chapter ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:keywords ], + sh:order 20 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 18 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; + sh:order 27 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path rdf:type ], + sh:order 22 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:mesh_terms ], + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:pages ] ; + sh:order 12 ; + sh:path biolink:format ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ] ; sh:targetClass biolink:BookChapter . biolink:CaseToDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association between a Case (patient) and a Disease" ; sh:closed true ; - sh:description "An association between a Case (patient) and a Disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_feature_name ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], + [ sh:class biolink:Disease ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 48 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:onset_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], + sh:order 37 ; + sh:path biolink:update_date ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ], + sh:order 49 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path dct:description ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], + sh:order 43 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:has_confidence_score ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:onset_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:order 42 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 46 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:sources ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ] ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:CaseToDiseaseAssociation . biolink:CaseToEntityAssociationMixin a sh:NodeShape ; + rdfs:comment "An abstract association for use where the case is the subject" ; sh:closed false ; - sh:description "An abstract association for use where the case is the subject" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -3837,87 +3867,101 @@ biolink:CaseToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:CaseToEntityAssociationMixin . biolink:CaseToGeneAssociation a sh:NodeShape ; + rdfs:comment "Association between a Case and a Gene (e.g., indicating a gene of interest for the case)" ; sh:closed true ; - sh:description "Association between a Case and a Gene (e.g., indicating a gene of interest for the case)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -3925,47 +3969,47 @@ biolink:CaseToGeneAssociation a sh:NodeShape ; sh:order 22 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; @@ -3973,92 +4017,80 @@ biolink:CaseToGeneAssociation a sh:NodeShape ; sh:order 40 ; sh:path biolink:semmed_agreement_count ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -4067,122 +4099,176 @@ biolink:CaseToGeneAssociation a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 26 ; + sh:path biolink:object_category_closure ] ; + sh:targetClass biolink:CaseToGeneAssociation . + +biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 54 ; + sh:path biolink:has_percentage ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 58 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; + sh:order 47 ; sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; + sh:order 25 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:CaseToGeneAssociation . - -biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 59 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_object ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:knowledge_level ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 61 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:category ], + sh:order 57 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:negated ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 43 ; + sh:path biolink:id ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category_closure ], + sh:order 4 ; + sh:path rdf:object ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -4190,107 +4276,107 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 23 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 6 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:supporting_text ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:update_date ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 2 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:has_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 45 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_feature_name ], + sh:order 46 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_feature_name ], + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 56 ; sh:path biolink:subject_direction_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 29 ; + sh:path biolink:subject_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence_of_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 61 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 58 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:id ], + sh:order 32 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 60 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -4298,284 +4384,212 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 49 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 51 ; + sh:path biolink:has_count ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:retrieval_source_ids ], + sh:order 1 ; + sh:path biolink:onset_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:deprecated ], + sh:order 41 ; + sh:path biolink:evidence_count ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 34 ; + sh:path biolink:p_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:onset_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_closure ], + sh:order 10 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 52 ; sh:path biolink:has_total ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdf:type ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 60 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:update_date ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 26 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 59 ; - sh:path biolink:qualified_predicate ] ; - sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . - -biolink:CaseToVariantAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Association between a Case and a Genetic Variant" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 39 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 21 ; sh:path biolink:subject_feature_name ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 30 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 55 ; + sh:path biolink:subject_aspect_qualifier ] ; + sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . + +biolink:CaseToVariantAssociation a sh:NodeShape ; + rdfs:comment "Association between a Case and a Genetic Variant" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; + sh:order 46 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], + sh:order 45 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -4583,193 +4597,184 @@ biolink:CaseToVariantAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:order 49 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 36 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], - [ sh:class biolink:Zygosity ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_zygosity ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:object_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], + sh:order 38 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:SequenceVariant ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], + sh:order 40 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 47 ; + sh:path dct:description ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 20 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:class biolink:SequenceVariant ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], + sh:order 44 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 48 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 37 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -4777,63 +4782,104 @@ biolink:CaseToVariantAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ] ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Zygosity ; + sh:description "The zygosity characterising a genotype or nucleic acid entity at a particular locus." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_zygosity ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ] ; sh:targetClass biolink:CaseToVariantAssociation . biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association between a gene and a disease where variation in the gene has been shown to have a causal role in the disease." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], + sh:order 21 ; + sh:path biolink:original_subject ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:object_category_closure ], + sh:order 26 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 52 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path rdfs:label ], + sh:order 32 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:allelic_requirement ; - sh:pattern "^HP:\\d{7}$" ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 15 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence_of_type ], + sh:order 7 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_feature_name ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -4841,374 +4887,515 @@ biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 24 ; + sh:path biolink:subject_feature_name ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:allelic_requirement ; + sh:pattern "^HP:\\d{7}$" ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:sources ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to cause the disease." ; + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_feature_name ], + sh:order 6 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 31 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 52 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_supporting_studies ], + sh:order 33 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 47 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 23 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdf:type ], + sh:order 35 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:subject_category_closure ], + sh:order 20 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:retrieval_source_ids ], + sh:order 49 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to cause the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 5 ; + sh:path rdf:subject ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], + sh:order 53 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 51 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:subject_category_closure ] ; + sh:targetClass biolink:CausalGeneToDiseaseAssociation . + +biolink:Cell a sh:NodeShape ; + rdfs:comment "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path rdf:object ], + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_closure ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_label_closure ], + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_closure ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; + sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:supporting_text ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:Cell . + +biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association in which a cell line - typically derived from an organismal entity with a disease state - serves as a model for that disease in experimental settings." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 11 ; - sh:path biolink:publications ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:path biolink:sources ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 42 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:update_date ], + sh:order 31 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:p_value ], + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_predicate ], + sh:order 5 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 53 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 55 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 19 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:CausalGeneToDiseaseAssociation . - -biolink:Cell a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 13 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 47 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 52 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 49 ; sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:information_content ], + sh:order 21 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 23 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 37 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 20 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 51 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_closure ], + [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Cell . - -biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -5216,163 +5403,150 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:evidence_count ], + sh:order 56 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], + sh:order 38 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:subject_specialization_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 56 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:qualified_predicate ], + sh:order 54 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path dct:description ], + sh:order 46 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 41 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:timepoint ], + sh:order 40 ; + sh:path biolink:update_date ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 22 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:update_date ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:sources ], + sh:order 57 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 58 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], + sh:order 43 ; + sh:path biolink:evidence_count ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 54 ; - sh:path biolink:subject_direction_qualifier ], + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "The relationship to the disease" ; + sh:in ( biolink:model_of ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 32 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], + sh:order 45 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 48 ; + sh:path rdf:type ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; @@ -5380,245 +5554,130 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 44 ; sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 14 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . + +biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; + sh:closed true ; + sh:ignoredProperties ( biolink:object_direction_qualifier biolink:subject_aspect_qualifier biolink:frequency_qualifier biolink:subject_direction_qualifier biolink:object_aspect_qualifier biolink:qualified_predicate rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:elevate_to_prediction ], + sh:order 37 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:category ], + sh:order 32 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 52 ; sh:path biolink:deprecated ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_specialization_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 21 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:disease_context_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], + sh:order 25 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_confidence_score ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], + sh:order 49 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "The relationship to the disease" ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_supporting_studies ] ; - sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . - -biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; - sh:ignoredProperties ( biolink:qualified_predicate biolink:subject_aspect_qualifier rdf:type biolink:object_aspect_qualifier biolink:subject_direction_qualifier biolink:frequency_qualifier biolink:object_direction_qualifier ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 48 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], + sh:order 34 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:sources ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], + sh:order 18 ; + sh:path biolink:agent_type ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; @@ -5631,161 +5690,161 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 51 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 22 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path dct:description ], + sh:order 41 ; + sh:path biolink:has_confidence_score ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_specialization_qualifier ], + sh:order 42 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], + sh:order 23 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], + sh:order 27 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 39 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 44 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 36 ; + sh:path biolink:p_value ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_confidence_score ], + sh:order 47 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], + sh:order 28 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:subject_specialization_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 50 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:evidence_count ], + sh:order 5 ; + sh:path biolink:object_specialization_qualifier ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -5793,76 +5852,34 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 46 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], + sh:order 14 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:knowledge_source ] ; + sh:order 11 ; + sh:path biolink:sources ] ; sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; + rdfs:comment "An relationship between a cell line and another entity" ; sh:closed false ; - sh:description "An relationship between a cell line and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:CellLine ; + sh:property [ sh:class biolink:CellLine ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -5875,280 +5892,239 @@ biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:CellLineToEntityAssociationMixin . biolink:CellularOrganism a sh:NodeShape ; + rdfs:comment "An organism that contains one or more cells belonging to the cellular lineages of life (Archaea, Bacteria, or Eukaryota), whose body consists of one or more cells. Distinguished from acellular biological entities such as viruses and viroids." ; sh:closed true ; - sh:description "" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 8 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:CellularOrganism . biolink:ChemicalAffectsBiologicalEntityAssociation a sh:NodeShape ; + rdfs:comment "Describes an effect that a chemical has on a biological entity (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; sh:closed true ; - sh:description "Describes an effect that a chemical has on a biological entity (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; - sh:ignoredProperties ( biolink:dgidb_interaction_score rdf:type biolink:supporting_documents biolink:dgidb_evidence_score ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:ignoredProperties ( biolink:dgidb_evidence_score rdf:type biolink:dgidb_interaction_score biolink:supporting_documents ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:affects biolink:ameliorates_condition biolink:disrupts biolink:exacerbates_condition biolink:has_adverse_event biolink:has_side_effect biolink:regulates ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 58 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path rdf:predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 33 ; + sh:path biolink:original_object ], [ sh:datatype xsd:anyURI ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:in ( biolink:causes ) ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:qualified_predicate ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 60 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:publications ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 46 ; - sh:path biolink:retrieval_source_ids ], + sh:order 47 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 41 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:negated ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 63 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:order 42 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A qualifier describing the context in which the subject of an association holds." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 49 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:species_context_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:has_confidence_score ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:order 58 ; + sh:path biolink:category ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:object_part_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 61 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:order 43 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:species_context_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "modulation" "allosteric_modulation" "mixed_allosteric_modulation" "biphasic_allosteric_modulation" "mixed_agonism" "positive_modulation" "potentiation" "induction" "cofactor" "activation" "positive_allosteric_modulation" "agonism" "partial_agonism" "biased_agonism" "antibody_agonism" "molecular_channel_opening" "stimulation" "guanyl_nucleotide_exchange" "negative_modulation" "negative_gene_editing_modulation" "gtpase_activation" "atpase_activation" "antisense_oligonucleotide_inhibition" "rna_interference_inhibition" "suppression" "feedback_inhibition" "inhibition" "antibody_inhibition" "antagonism" "allosteric_antagonism" "non_competitive_antagonism" "competitive_inhibition" "noncompetitive_inhibition" "negative_allosteric_modulation" "gating_inhibition" "irreversible_inhibition" "molecular_channel_blockage" "inverse_agonism" "binding" "covalent_binding" "adduction" "crosslinking" "transglutamination" "disuphide_binding" "stabilization" "chaperone_mediated_stabilization" "destabilization" "degradation" "cleavage" "hydrolysis" "disruption" "opening" "multitarget_modulation" "chelation" "release" "sequestration" "oxidoreduction" "exogenous_protein" "exogenous_gene" "transcriptional_regulation" "translational_regulation" "catalytic_activity" "chemical_modification" "relocalization" "isomerization" "signaling_mediated_control" "immune_system_modulation" "vaccine_antigen" "post_transcriptional_regulation" "molecular_modification" "phosphorylation" "dephosphorylation" "neddylation" "deneddylation" "lipidation" "palmitoylation" "myristoylation" "tyrosination" "carboxylation" "ubiquitination" "monoubiquitination" "polyubiquitination" "deubiquitination" "sulfation" "reduction" "oxidation" "acetylation" "deacetylation" "glycosylation" "deglycosylation" "methylation" "trimethylation" "demethylation" "sumoylation" "desumoylation" "ADP-ribosylation" "de-ADP-ribosylation" "ampylation" "hydroxylation" "s_nitrosylation" ) ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:subject_category ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:nodeKind sh:Literal ; + sh:order 55 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:predicate ], + sh:order 54 ; + sh:path biolink:evidence_count ], [ sh:class biolink:BiologicalEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -6156,17 +6132,16 @@ biolink:ChemicalAffectsBiologicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_feature_name ], + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_label_closure ], + sh:order 39 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6174,48 +6149,33 @@ biolink:ChemicalAffectsBiologicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 56 ; sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:sources ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 59 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 63 ; + sh:path biolink:deprecated ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:sources ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -6223,83 +6183,130 @@ biolink:ChemicalAffectsBiologicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path rdf:subject ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 50 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 61 ; + sh:path dct:description ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:AnatomicalEntity ; + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 29 ; - sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:evidence_count ], + sh:order 23 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:original_predicate ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:subject_closure ], + sh:order 27 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:original_object ], + sh:order 26 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 60 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 62 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:object_closure ], + sh:order 35 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 46 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:object_label_closure ], + sh:order 30 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -6307,82 +6314,128 @@ biolink:ChemicalAffectsBiologicalEntityAssociation a sh:NodeShape ; sh:order 57 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:update_date ], + sh:order 59 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:object_category ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A qualifier describing the context in which the object of an association holds." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 50 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:knowledge_level ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" ; + sh:in ( "modulation" "allosteric_modulation" "mixed_allosteric_modulation" "biphasic_allosteric_modulation" "mixed_agonism" "positive_modulation" "potentiation" "induction" "cofactor" "activation" "positive_allosteric_modulation" "agonism" "partial_agonism" "biased_agonism" "antibody_agonism" "molecular_channel_opening" "stimulation" "guanyl_nucleotide_exchange" "negative_modulation" "negative_gene_editing_modulation" "gtpase_activation" "atpase_activation" "antisense_oligonucleotide_inhibition" "rna_interference_inhibition" "suppression" "feedback_inhibition" "inhibition" "antibody_inhibition" "antagonism" "allosteric_antagonism" "non_competitive_antagonism" "competitive_inhibition" "noncompetitive_inhibition" "negative_allosteric_modulation" "gating_inhibition" "irreversible_inhibition" "molecular_channel_blockage" "inverse_agonism" "binding" "covalent_binding" "adduction" "crosslinking" "transglutamination" "disuphide_binding" "stabilization" "chaperone_mediated_stabilization" "destabilization" "degradation" "cleavage" "hydrolysis" "disruption" "opening" "multitarget_modulation" "chelation" "release" "sequestration" "oxidoreduction" "exogenous_protein" "exogenous_gene" "transcriptional_regulation" "translational_regulation" "catalytic_activity" "chemical_modification" "relocalization" "isomerization" "signaling_mediated_control" "immune_system_modulation" "vaccine_antigen" "post_transcriptional_regulation" "molecular_modification" "phosphorylation" "dephosphorylation" "neddylation" "deneddylation" "lipidation" "palmitoylation" "myristoylation" "tyrosination" "carboxylation" "ubiquitination" "monoubiquitination" "polyubiquitination" "deubiquitination" "sulfation" "reduction" "oxidation" "acetylation" "deacetylation" "glycosylation" "deglycosylation" "methylation" "trimethylation" "demethylation" "sumoylation" "desumoylation" "ADP-ribosylation" "de-ADP-ribosylation" "ampylation" "hydroxylation" "s_nitrosylation" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:p_value ] ; + sh:order 53 ; + sh:path biolink:elevate_to_prediction ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ] ; sh:targetClass biolink:ChemicalAffectsBiologicalEntityAssociation . biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; + rdfs:comment "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; sh:closed true ; - sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 54 ; - sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 63 ; sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 50 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:AnatomicalEntity ; + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:object_context_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:order 5 ; + sh:path biolink:subject_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_form_or_variant_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 66 ; + sh:path biolink:deprecated ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6391,402 +6444,419 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:order 59 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:qualifier ], + sh:order 34 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "A score defined by DGIdb that is used to rank interaction record results in DGIdb, which combines their evidence score (based on total supporting sources and pubs), with their relative gene specificity score and relative drug specificity score. See https://dgidb.org/about/overview/interaction-score." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:dgidb_interaction_score ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" ; + sh:in ( "modulation" "allosteric_modulation" "mixed_allosteric_modulation" "biphasic_allosteric_modulation" "mixed_agonism" "positive_modulation" "potentiation" "induction" "cofactor" "activation" "positive_allosteric_modulation" "agonism" "partial_agonism" "biased_agonism" "antibody_agonism" "molecular_channel_opening" "stimulation" "guanyl_nucleotide_exchange" "negative_modulation" "negative_gene_editing_modulation" "gtpase_activation" "atpase_activation" "antisense_oligonucleotide_inhibition" "rna_interference_inhibition" "suppression" "feedback_inhibition" "inhibition" "antibody_inhibition" "antagonism" "allosteric_antagonism" "non_competitive_antagonism" "competitive_inhibition" "noncompetitive_inhibition" "negative_allosteric_modulation" "gating_inhibition" "irreversible_inhibition" "molecular_channel_blockage" "inverse_agonism" "binding" "covalent_binding" "adduction" "crosslinking" "transglutamination" "disuphide_binding" "stabilization" "chaperone_mediated_stabilization" "destabilization" "degradation" "cleavage" "hydrolysis" "disruption" "opening" "multitarget_modulation" "chelation" "release" "sequestration" "oxidoreduction" "exogenous_protein" "exogenous_gene" "transcriptional_regulation" "translational_regulation" "catalytic_activity" "chemical_modification" "relocalization" "isomerization" "signaling_mediated_control" "immune_system_modulation" "vaccine_antigen" "post_transcriptional_regulation" "molecular_modification" "phosphorylation" "dephosphorylation" "neddylation" "deneddylation" "lipidation" "palmitoylation" "myristoylation" "tyrosination" "carboxylation" "ubiquitination" "monoubiquitination" "polyubiquitination" "deubiquitination" "sulfation" "reduction" "oxidation" "acetylation" "deacetylation" "glycosylation" "deglycosylation" "methylation" "trimethylation" "demethylation" "sumoylation" "desumoylation" "ADP-ribosylation" "de-ADP-ribosylation" "ampylation" "hydroxylation" "s_nitrosylation" ) ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "A qualifier describing the context in which the object of an association holds." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 13 ; + sh:path biolink:object_context_qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:species_context_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 58 ; sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:original_subject ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:order 62 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:in ( biolink:causes ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 41 ; sh:path biolink:object_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 32 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:timepoint ], + sh:order 30 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:original_object ], + [ sh:datatype xsd:integer ; + sh:description "A score defined by DGIdb that is used to report the amount of evidence supporting a given interaction statement, which is simply the sum of all supporting sources and publications. See https://dgidb.org/about/overview/interaction-score." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:dgidb_evidence_score ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 54 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A qualifier describing the context in which the subject of an association holds." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:subject_context_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:has_evidence_of_type ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 47 ; sh:path biolink:object_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 50 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 45 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:update_date ], + sh:order 31 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 65 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:qualified_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:object_closure ], + sh:order 64 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:elevate_to_prediction ], + sh:order 22 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 60 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 56 ; sh:path biolink:has_confidence_score ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:BiologicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 21 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 44 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:primary_knowledge_source ], + sh:order 39 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_part_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:supporting_text ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "One or more referenceable documents that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:supporting_documents ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:order 23 ; + sh:path biolink:qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:integer ; - sh:description "A score defined by DGIdb that is used to report the amount of evidence supporting a given interaction statement, which is simply the sum of all supporting sources and publications. See https://dgidb.org/about/overview/interaction-score." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:dgidb_evidence_score ], + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 33 ; sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 66 ; - sh:path biolink:deprecated ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path rdf:subject ], - [ sh:class biolink:BiologicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 64 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 62 ; - sh:path rdf:type ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:qualifiers ], + sh:order 55 ; + sh:path biolink:update_date ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:affects biolink:ameliorates_condition biolink:disrupts biolink:exacerbates_condition biolink:has_adverse_event biolink:has_side_effect biolink:regulates ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 45 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 60 ; - sh:path biolink:iri ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 57 ; + sh:path biolink:elevate_to_prediction ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:sources ], + [ sh:datatype xsd:anyURI ; + sh:description "One or more referenceable documents that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:evidence_count ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "modulation" "allosteric_modulation" "mixed_allosteric_modulation" "biphasic_allosteric_modulation" "mixed_agonism" "positive_modulation" "potentiation" "induction" "cofactor" "activation" "positive_allosteric_modulation" "agonism" "partial_agonism" "biased_agonism" "antibody_agonism" "molecular_channel_opening" "stimulation" "guanyl_nucleotide_exchange" "negative_modulation" "negative_gene_editing_modulation" "gtpase_activation" "atpase_activation" "antisense_oligonucleotide_inhibition" "rna_interference_inhibition" "suppression" "feedback_inhibition" "inhibition" "antibody_inhibition" "antagonism" "allosteric_antagonism" "non_competitive_antagonism" "competitive_inhibition" "noncompetitive_inhibition" "negative_allosteric_modulation" "gating_inhibition" "irreversible_inhibition" "molecular_channel_blockage" "inverse_agonism" "binding" "covalent_binding" "adduction" "crosslinking" "transglutamination" "disuphide_binding" "stabilization" "chaperone_mediated_stabilization" "destabilization" "degradation" "cleavage" "hydrolysis" "disruption" "opening" "multitarget_modulation" "chelation" "release" "sequestration" "oxidoreduction" "exogenous_protein" "exogenous_gene" "transcriptional_regulation" "translational_regulation" "catalytic_activity" "chemical_modification" "relocalization" "isomerization" "signaling_mediated_control" "immune_system_modulation" "vaccine_antigen" "post_transcriptional_regulation" "molecular_modification" "phosphorylation" "dephosphorylation" "neddylation" "deneddylation" "lipidation" "palmitoylation" "myristoylation" "tyrosination" "carboxylation" "ubiquitination" "monoubiquitination" "polyubiquitination" "deubiquitination" "sulfation" "reduction" "oxidation" "acetylation" "deacetylation" "glycosylation" "deglycosylation" "methylation" "trimethylation" "demethylation" "sumoylation" "desumoylation" "ADP-ribosylation" "de-ADP-ribosylation" "ampylation" "hydroxylation" "s_nitrosylation" ) ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:order 3 ; + sh:path biolink:supporting_documents ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 61 ; sh:path biolink:category ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_part_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:p_value ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:species_context_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 6 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_part_qualifier ] ; + sh:order 9 ; + sh:path biolink:subject_direction_qualifier ] ; sh:targetClass biolink:ChemicalAffectsGeneAssociation . biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -6798,230 +6868,290 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:was_tested_for_effect_on ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path biolink:subject_label_closure ] ; + sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . + +biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; + rdfs:comment "A regulatory relationship between two genes" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 43 ; + sh:path biolink:iri ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 45 ; - sh:path rdfs:label ], + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 21 ; + sh:path biolink:object_feature_name ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 8 ; sh:path biolink:sources ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 15 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:path biolink:update_date ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 47 ; + sh:order 48 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:path biolink:subject_label_closure ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ] ; - sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . - -biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A regulatory relationship between two genes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -7029,74 +7159,105 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:nodeKind sh:BlankNodeOrIRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:anyURI ; + sh:description "the direction is always from regulator to regulated" ; + sh:in ( biolink:regulates ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 40 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:category ], + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; @@ -7104,226 +7265,219 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:order 20 ; sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:supporting_text ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:object_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 44 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], + sh:order 47 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 46 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 42 ; + sh:path biolink:id ] ; + sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + +biolink:ChemicalEntityToBiologicalProcessAssociation a sh:NodeShape ; + rdfs:comment "An association between a chemical entity and a biological process, where the chemical entity has some effect on the biological process." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], + sh:order 40 ; + sh:path biolink:update_date ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 51 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], + sh:order 7 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], + sh:order 25 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], + sh:order 14 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:order 28 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:order 48 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 0 ; + sh:path biolink:species_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], + sh:order 42 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 36 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "the direction is always from regulator to regulated" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], + sh:order 46 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 31 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 39 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . - -biolink:ChemicalEntityToBiologicalProcessAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a chemical entity and a biological process, where the chemical entity has some effect on the biological process." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 38 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 41 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:active_in biolink:actively_involved_in biolink:actively_involves biolink:acts_upstream_of biolink:acts_upstream_of_negative_effect biolink:acts_upstream_of_or_within biolink:acts_upstream_of_or_within_negative_effect biolink:acts_upstream_of_or_within_positive_effect biolink:acts_upstream_of_positive_effect biolink:adverse_event_of biolink:affected_by biolink:affects biolink:affects_likelihood_of biolink:affects_sensitivity_to biolink:ameliorates_condition biolink:amount_or_activity_decreased_by biolink:amount_or_activity_increased_by biolink:applied_to_treat biolink:associated_with biolink:associated_with_decreased_likelihood_of biolink:associated_with_increased_likelihood_of biolink:associated_with_likelihood_of biolink:associated_with_resistance_to biolink:associated_with_response_to biolink:associated_with_sensitivity_to biolink:author biolink:beneficial_in_models_for biolink:binds biolink:biomarker_for biolink:can_be_carried_out_by biolink:capable_of biolink:catalyzes biolink:caused_by biolink:causes biolink:chemically_similar_to biolink:coexists_with biolink:coexpressed_with biolink:colocalizes_with biolink:completed_by biolink:condition_ameliorated_by biolink:condition_associated_with_gene biolink:condition_exacerbated_by biolink:condition_predisposed_by biolink:condition_prevented_by biolink:condition_promoted_by biolink:consumed_by biolink:consumes biolink:contains_process biolink:contraindicated_in biolink:contributes_to biolink:contribution_from biolink:contributor biolink:correlated_with biolink:decreased_amount_in biolink:decreased_likelihood_associated_with biolink:decreases_amount_or_activity_of biolink:decreases_sensitivity_to biolink:derives_from biolink:derives_into biolink:develops_from biolink:develops_into biolink:diagnoses biolink:directly_physically_interacts_with biolink:disease_has_basis_in biolink:disrupted_by biolink:disrupts biolink:editor biolink:enabled_by biolink:enables biolink:exacerbates_condition biolink:expressed_in biolink:expresses biolink:food_component_of biolink:gene_associated_with_condition biolink:gene_fusion_with biolink:gene_product_of biolink:genetic_association biolink:genetic_neighborhood_of biolink:genetically_associated_with biolink:genetically_interacts_with biolink:has_active_component biolink:has_active_ingredient biolink:has_adverse_event biolink:has_author biolink:has_biomarker biolink:has_catalyst biolink:has_completed biolink:has_contraindication biolink:has_contributor biolink:has_decreased_amount biolink:has_editor biolink:has_excipient biolink:has_food_component biolink:has_frameshift_variant biolink:has_gene_product biolink:has_increased_amount biolink:has_input biolink:has_manifestation biolink:has_metabolite biolink:has_missense_variant biolink:has_mode_of_inheritance biolink:has_molecular_consequence biolink:has_nearby_variant biolink:has_negative_upstream_actor biolink:has_negative_upstream_or_within_actor biolink:has_non_coding_variant biolink:has_nonsense_variant biolink:has_not_completed biolink:has_nutrient biolink:has_output biolink:has_part biolink:has_participant biolink:has_phenotype biolink:has_plasma_membrane_part biolink:has_positive_upstream_actor biolink:has_positive_upstream_or_within_actor biolink:has_provider biolink:has_publisher biolink:has_sequence_location biolink:has_sequence_variant biolink:has_side_effect biolink:has_splice_site_variant biolink:has_substrate biolink:has_synonymous_variant biolink:has_target biolink:has_upstream_actor biolink:has_upstream_or_within_actor biolink:has_variant_part biolink:homologous_to biolink:in_cell_population_with biolink:in_clinical_trials_for biolink:in_complex_with biolink:in_linkage_disequilibrium_with biolink:in_pathway_with biolink:in_preclinical_trials_for biolink:in_taxon biolink:increased_amount_of biolink:increased_likelihood_associated_with biolink:increases_amount_or_activity_of biolink:increases_sensitivity_to biolink:indirectly_physically_interacts_with biolink:interacts_with biolink:is_active_ingredient_of biolink:is_diagnosed_by biolink:is_excipient_of biolink:is_frameshift_variant_of biolink:is_input_of biolink:is_metabolite_of biolink:is_missense_variant_of biolink:is_molecular_consequence_of biolink:is_nearby_variant_of biolink:is_non_coding_variant_of biolink:is_nonsense_variant_of biolink:is_output_of biolink:is_sequence_variant_of biolink:is_side_effect_of biolink:is_splice_site_variant_of biolink:is_substrate_of biolink:is_synonymous_variant_of biolink:lacks_part biolink:likelihood_affected_by biolink:likelihood_associated_with biolink:located_in biolink:location_of biolink:manifestation_of biolink:mentioned_by biolink:mentions biolink:missing_from biolink:mode_of_inheritance_of biolink:model_of biolink:models biolink:models_demonstrating_benefits_for biolink:negatively_correlated_with biolink:not_completed_by biolink:nutrient_of biolink:occurs_in biolink:occurs_in_disease biolink:occurs_together_in_literature_with biolink:opposite_of biolink:orthologous_to biolink:overlaps biolink:paralogous_to biolink:part_of biolink:participates_in biolink:pharmacologically_interacts_with biolink:phenotype_of biolink:physically_interacts_with biolink:plasma_membrane_part_of biolink:positively_correlated_with biolink:preceded_by biolink:precedes biolink:predisposes_to_condition biolink:preventative_for_condition biolink:produced_by biolink:produces biolink:promotes_condition biolink:provider biolink:publisher biolink:regulated_by biolink:regulates biolink:related_condition biolink:related_to_at_instance_level biolink:resistance_associated_with biolink:response_associated_with biolink:sensitivity_affected_by biolink:sensitivity_associated_with biolink:sensitivity_decreased_by biolink:sensitivity_increased_by biolink:sequence_location_of biolink:similar_to biolink:studied_to_treat biolink:subject_of_treatment_application_or_study_for_treatment_by biolink:target_for biolink:taxon_of biolink:temporally_related_to biolink:tested_by_clinical_trials_of biolink:tested_by_preclinical_trials_of biolink:transcribed_from biolink:transcribed_to biolink:translates_to biolink:translation_of biolink:treated_by biolink:treated_in_studies_by biolink:treatment_applications_from biolink:treats biolink:treats_or_applied_or_studied_to_treat biolink:variant_part_of biolink:was_tested_for_effect_of biolink:was_tested_for_effect_on biolink:xenologous_to ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:evidence_count ], + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that affects the biological process" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:sources ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; @@ -7331,387 +7485,333 @@ biolink:ChemicalEntityToBiologicalProcessAssociation a sh:NodeShape ; sh:order 23 ; sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 49 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:update_date ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence_of_type ], + sh:order 37 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:elevate_to_prediction ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:species_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], + sh:order 24 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdfs:label ], + sh:order 45 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 19 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 52 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], + sh:order 2 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that affects the biological process" ; + sh:order 43 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:BiologicalProcess ; + sh:description "the biological process that is affected by the chemical entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_supporting_studies ], + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_confidence_score ], + sh:order 21 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:deprecated ], + sh:order 32 ; + sh:path biolink:object_namespace ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 18 ; sh:path biolink:agent_type ], - [ sh:class biolink:BiologicalProcess ; - sh:description "the biological process that is affected by the chemical entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:sources ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:qualifiers ], + sh:path biolink:qualifiers ] ; + sh:targetClass biolink:ChemicalEntityToBiologicalProcessAssociation . + +biolink:ChemicalEntityToChemicalDerivationAssociation a sh:NodeShape ; + rdfs:comment "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:catalyst_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 21 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 5 ; + sh:path biolink:negated ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 32 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], + sh:order 47 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; + sh:order 17 ; sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:order 24 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:update_date ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], + sh:order 50 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:qualified_predicate ] ; - sh:targetClass biolink:ChemicalEntityToBiologicalProcessAssociation . - -biolink:ChemicalEntityToChemicalDerivationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path rdfs:label ], + sh:order 44 ; + sh:path biolink:iri ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 46 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:semmed_agreement_count ], + sh:order 43 ; + sh:path biolink:id ], [ sh:class biolink:ChemicalEntity ; - sh:description "the downstream chemical entity" ; + sh:description "the upstream chemical entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:derives_into biolink:has_metabolite ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 49 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_closure ], + sh:order 41 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_feature_name ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category ], + sh:order 28 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdf:type ], + sh:order 30 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -7725,241 +7825,152 @@ biolink:ChemicalEntityToChemicalDerivationAssociation a sh:NodeShape ; sh:order 20 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_feature_name ], + sh:order 26 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path dct:description ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the upstream chemical entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category ], + sh:order 8 ; + sh:path biolink:publications ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_namespace ], + sh:order 31 ; + sh:path biolink:subject_label_closure ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:catalyst_qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_subject ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], + sh:order 4 ; + sh:path biolink:species_context_qualifier ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 35 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 39 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the downstream chemical entity" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_namespace ] ; + sh:order 25 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:ChemicalEntityToChemicalDerivationAssociation . biolink:ChemicalEntityToChemicalEntityAssociation a sh:NodeShape ; + rdfs:comment "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; sh:closed true ; - sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; - sh:ignoredProperties ( biolink:reaction_direction rdf:type biolink:stoichiometry biolink:reaction_side biolink:catalyst_qualifier ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:ignoredProperties ( biolink:catalyst_qualifier biolink:reaction_direction rdf:type biolink:reaction_side biolink:stoichiometry ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:supporting_text ], + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 48 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 44 ; + sh:path biolink:category ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -7968,28 +7979,27 @@ biolink:ChemicalEntityToChemicalEntityAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; @@ -8001,91 +8011,63 @@ biolink:ChemicalEntityToChemicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], + sh:order 36 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -8094,11 +8076,44 @@ biolink:ChemicalEntityToChemicalEntityAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -8106,393 +8121,422 @@ biolink:ChemicalEntityToChemicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 43 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], + sh:order 38 ; + sh:path biolink:has_confidence_score ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 20 ; + sh:path biolink:subject_feature_name ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:object_feature_name ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 47 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; + sh:order 49 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ] ; + sh:order 35 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:ChemicalEntityToChemicalEntityAssociation . biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:closed true ; - sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:iri ], + sh:order 21 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 47 ; + sh:path biolink:id ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category ], + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 54 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path rdf:type ], - [ sh:description "The clinical approval status of a chemical entity for treating a specific disease or condition, as captured in the context of the association between the chemical and the disease." ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 37 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 40 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 52 ; sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:order 28 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:subject_specialization_qualifier ], + sh:order 44 ; + sh:path biolink:elevate_to_prediction ], [ sh:description "The maximum research phase reached for a specific chemical-disease pair, indicating the highest clinical trial phase achieved for the chemical entity's investigation as a treatment for the associated disease or condition." ; sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_1_to_2" "clinical_trial_phase_2" "clinical_trial_phase_2_to_3" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:max_research_phase ], - [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:sources ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 34 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:semmed_agreement_count ], + sh:order 42 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:supporting_text ], + sh:order 10 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_predicate ], + sh:order 17 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path rdfs:label ], + sh:order 30 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:object_specialization_qualifier ], + sh:order 6 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 24 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_confidence_score ], + sh:order 51 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:category ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:disease_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 26 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 14 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:primary_knowledge_source ], + sh:order 7 ; + sh:path biolink:object_specialization_qualifier ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 53 ; - sh:path biolink:has_attribute ], + sh:order 9 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:sources ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:update_date ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 50 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:retrieval_source_ids ], + sh:order 3 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 29 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 45 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:deprecated ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 43 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_closure ], + sh:order 46 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_closure ], + sh:order 18 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 53 ; + sh:path biolink:has_attribute ], + [ sh:description "The clinical approval status of a chemical entity for treating a specific disease or condition, as captured in the context of the association between the chemical and the disease." ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "the disease or phenotype that is affected by the chemical" ; + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:order 38 ; + sh:path biolink:p_value ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -8500,32 +8544,18 @@ biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 20 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_feature_name ] ; + sh:order 25 ; + sh:path biolink:subject_feature_name ] ; sh:targetClass biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; + rdfs:comment "An interaction between a chemical entity and another entity" ; sh:closed false ; - sh:description "An interaction between a chemical entity and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -8538,411 +8568,369 @@ biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . biolink:ChemicalEntityToPathwayAssociation a sh:NodeShape ; + rdfs:comment "An interaction between a chemical entity and a biological process or pathway." ; sh:closed true ; - sh:description "An interaction between a chemical entity and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 46 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that is affecting the pathway" ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that is affected by the chemical" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 43 ; + sh:path biolink:category ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that is affected by the chemical" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdfs:label ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that is affecting the pathway" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ChemicalEntityToPathwayAssociation . - -biolink:ChemicalExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical exposure is an intake of a particular chemical entity." ; - sh:ignoredProperties ( biolink:has_gene_or_gene_product rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:exposure_additional_condition ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:taxon ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ] ; + sh:targetClass biolink:ChemicalEntityToPathwayAssociation . + +biolink:ChemicalExposure a sh:NodeShape ; + rdfs:comment "A chemical exposure is an intake of a particular chemical entity." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type biolink:has_gene_or_gene_product ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:exposure_magnitude ], - [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:exposure_end_age ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:exposure_duration ], + [ sh:datatype xsd:string ; + sh:description "Route of exposure." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:exposure_route ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:exposure_type ], - [ sh:datatype xsd:string ; - sh:description "Type of an exposure event." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:exposure_vehicle ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + sh:order 12 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; + sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; - sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:exposure_additional_condition ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:exposure_duration ], + sh:order 20 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; sh:maxCount 1 ; @@ -8950,18 +8938,6 @@ biolink:ChemicalExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:exposure_route ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; @@ -8973,205 +8949,175 @@ biolink:ChemicalExposure a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:ChemicalExposure . - -biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "describes an interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 14 ; + sh:path biolink:synonym ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 46 ; - sh:path biolink:retrieval_source_ids ], + sh:order 23 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:iri ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:order 1 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Type of an exposure event." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:exposure_vehicle ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 17 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 50 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:integer ; + sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:AffinityMeasurement ; - sh:description "Set of measurements documenting the strength of chemical entity to gene or gene product interactions." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_affinity ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:exposure_start_age ], + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 6 ; + sh:path biolink:exposure_end_age ] ; + sh:targetClass biolink:ChemicalExposure . + +biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; + rdfs:comment "describes an interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:object_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 47 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 56 ; - sh:path biolink:id ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 29 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 23 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 50 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A qualifier describing the context in which the subject of an association holds." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 20 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 61 ; - sh:path dct:description ], + sh:order 55 ; + sh:path biolink:semmed_agreement_count ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 40 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:original_predicate ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:order 54 ; + sh:path biolink:evidence_count ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:subject_part_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:update_date ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 60 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:publications ], + sh:order 62 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 49 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 59 ; - sh:path rdf:type ], + sh:order 32 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 5 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 60 ; - sh:path rdfs:label ], + sh:order 51 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -9184,204 +9130,275 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 63 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 58 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A score defined by DGIdb that is used to rank interaction record results in DGIdb, which combines their evidence score (based on total supporting sources and pubs), with their relative gene specificity score and relative drug specificity score. See https://dgidb.org/about/overview/interaction-score." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:original_object ], + sh:order 13 ; + sh:path biolink:dgidb_interaction_score ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:object_category ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" ; + sh:in ( "modulation" "allosteric_modulation" "mixed_allosteric_modulation" "biphasic_allosteric_modulation" "mixed_agonism" "positive_modulation" "potentiation" "induction" "cofactor" "activation" "positive_allosteric_modulation" "agonism" "partial_agonism" "biased_agonism" "antibody_agonism" "molecular_channel_opening" "stimulation" "guanyl_nucleotide_exchange" "negative_modulation" "negative_gene_editing_modulation" "gtpase_activation" "atpase_activation" "antisense_oligonucleotide_inhibition" "rna_interference_inhibition" "suppression" "feedback_inhibition" "inhibition" "antibody_inhibition" "antagonism" "allosteric_antagonism" "non_competitive_antagonism" "competitive_inhibition" "noncompetitive_inhibition" "negative_allosteric_modulation" "gating_inhibition" "irreversible_inhibition" "molecular_channel_blockage" "inverse_agonism" "binding" "covalent_binding" "adduction" "crosslinking" "transglutamination" "disuphide_binding" "stabilization" "chaperone_mediated_stabilization" "destabilization" "degradation" "cleavage" "hydrolysis" "disruption" "opening" "multitarget_modulation" "chelation" "release" "sequestration" "oxidoreduction" "exogenous_protein" "exogenous_gene" "transcriptional_regulation" "translational_regulation" "catalytic_activity" "chemical_modification" "relocalization" "isomerization" "signaling_mediated_control" "immune_system_modulation" "vaccine_antigen" "post_transcriptional_regulation" "molecular_modification" "phosphorylation" "dephosphorylation" "neddylation" "deneddylation" "lipidation" "palmitoylation" "myristoylation" "tyrosination" "carboxylation" "ubiquitination" "monoubiquitination" "polyubiquitination" "deubiquitination" "sulfation" "reduction" "oxidation" "acetylation" "deacetylation" "glycosylation" "deglycosylation" "methylation" "trimethylation" "demethylation" "sumoylation" "desumoylation" "ADP-ribosylation" "de-ADP-ribosylation" "ampylation" "hydroxylation" "s_nitrosylation" ) ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:timepoint ], + sh:order 44 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:binds biolink:directly_physically_interacts_with biolink:gene_fusion_with biolink:genetic_neighborhood_of biolink:genetically_interacts_with biolink:indirectly_physically_interacts_with biolink:interacts_with biolink:pharmacologically_interacts_with biolink:physically_interacts_with biolink:regulates ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:predicate ], [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "modulation" "allosteric_modulation" "mixed_allosteric_modulation" "biphasic_allosteric_modulation" "mixed_agonism" "positive_modulation" "potentiation" "induction" "cofactor" "activation" "positive_allosteric_modulation" "agonism" "partial_agonism" "biased_agonism" "antibody_agonism" "molecular_channel_opening" "stimulation" "guanyl_nucleotide_exchange" "negative_modulation" "negative_gene_editing_modulation" "gtpase_activation" "atpase_activation" "antisense_oligonucleotide_inhibition" "rna_interference_inhibition" "suppression" "feedback_inhibition" "inhibition" "antibody_inhibition" "antagonism" "allosteric_antagonism" "non_competitive_antagonism" "competitive_inhibition" "noncompetitive_inhibition" "negative_allosteric_modulation" "gating_inhibition" "irreversible_inhibition" "molecular_channel_blockage" "inverse_agonism" "binding" "covalent_binding" "adduction" "crosslinking" "transglutamination" "disuphide_binding" "stabilization" "chaperone_mediated_stabilization" "destabilization" "degradation" "cleavage" "hydrolysis" "disruption" "opening" "multitarget_modulation" "chelation" "release" "sequestration" "oxidoreduction" "exogenous_protein" "exogenous_gene" "transcriptional_regulation" "translational_regulation" "catalytic_activity" "chemical_modification" "relocalization" "isomerization" "signaling_mediated_control" "immune_system_modulation" "vaccine_antigen" "post_transcriptional_regulation" "molecular_modification" "phosphorylation" "dephosphorylation" "neddylation" "deneddylation" "lipidation" "palmitoylation" "myristoylation" "tyrosination" "carboxylation" "ubiquitination" "monoubiquitination" "polyubiquitination" "deubiquitination" "sulfation" "reduction" "oxidation" "acetylation" "deacetylation" "glycosylation" "deglycosylation" "methylation" "trimethylation" "demethylation" "sumoylation" "desumoylation" "ADP-ribosylation" "de-ADP-ribosylation" "ampylation" "hydroxylation" "s_nitrosylation" ) ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "A qualifier describing the context in which the object of an association holds." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 58 ; - sh:path biolink:category ], + sh:order 59 ; + sh:path rdf:type ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:object_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A score defined by DGIdb that is used to rank interaction record results in DGIdb, which combines their evidence score (based on total supporting sources and pubs), with their relative gene specificity score and relative drug specificity score. See https://dgidb.org/about/overview/interaction-score." ; - sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:dgidb_interaction_score ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 30 ; + sh:path biolink:timepoint ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 3 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:sources ], + sh:order 33 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:object_namespace ], + sh:order 26 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:supporting_text ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 57 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:object_part_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:elevate_to_prediction ], + sh:order 52 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:object_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 18 ; + sh:path biolink:negated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 17 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:evidence_count ], + sh:order 35 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:object_closure ], + sh:order 61 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:sources ], [ sh:datatype xsd:integer ; sh:description "A score defined by DGIdb that is used to report the amount of evidence supporting a given interaction statement, which is simply the sum of all supporting sources and publications. See https://dgidb.org/about/overview/interaction-score." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:dgidb_evidence_score ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 46 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 56 ; + sh:path biolink:id ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 24 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 62 ; - sh:path biolink:has_attribute ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; + sh:order 41 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_derivative_qualifier ] ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:AffinityMeasurement ; + sh:description "Set of measurements documenting the strength of chemical entity to gene or gene product interactions." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_affinity ] ; sh:targetClass biolink:ChemicalGeneInteractionAssociation . biolink:ChemicalMixture a sh:NodeShape ; + rdfs:comment "A chemical mixture is a chemical entity composed of two or more molecular entities." ; sh:closed true ; - sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a chemical entity is a natural product." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path biolink:chembl_natural_product ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:chembl_prodrug ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; - sh:order 9 ; - sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; @@ -9391,17 +9408,35 @@ biolink:ChemicalMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path rdfs:label ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "Tern indicating the chirality of the chemical entity." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:chembl_chirality ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; @@ -9409,17 +9444,17 @@ biolink:ChemicalMixture a sh:NodeShape ; sh:order 21 ; sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:chembl_black_box_warning ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:chembl_drug_warning ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; @@ -9430,62 +9465,53 @@ biolink:ChemicalMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a chemical entity is a natural product." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:chembl_natural_product ], - [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; + sh:order 9 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:chembl_drug_warning ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:order 22 ; + sh:path biolink:taxon ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "Text indicating the availability type of the chemical entity." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:chembl_availability_type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 25 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:chembl_black_box_warning ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -9493,69 +9519,92 @@ biolink:ChemicalMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Text indicating the availability type of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:chembl_availability_type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Tern indicating the chirality of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "" ; + sh:order 14 ; + sh:path biolink:chembl_chirality ], + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ] ; + sh:order 10 ; + sh:path biolink:chembl_prodrug ] ; sh:targetClass biolink:ChemicalMixture . biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; + rdfs:comment "A mixin for entities that represent chemical substances, pharmacological agents, or therapeutic interventions." ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:ChemicalOrDrugOrTreatment . biolink:ChemicalOrDrugOrTreatmentAdverseEventAssociation a sh:NodeShape ; + rdfs:comment "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an untoward medical occurrence that happens during treatment, whether or not considered related to the treatment." ; sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an untoward medical occurrence that happens during treatment, whether or not considered related to the treatment." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:category ], + sh:order 52 ; + sh:path biolink:iri ], + [ sh:description "The level or severity grade of an adverse event as classified by FDA adverse-event terminology, drawn from FDAIDAAdverseEventEnum; used on adverse-event associations." ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], [ sh:datatype xsd:anyURI ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:qualified_predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 59 ; - sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 40 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:supporting_text ], + sh:order 14 ; + sh:path biolink:qualifier ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -9563,396 +9612,339 @@ biolink:ChemicalOrDrugOrTreatmentAdverseEventAssociation a sh:NodeShape ; sh:order 23 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 37 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:qualifier ], + sh:order 17 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:object_namespace ], + sh:order 44 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_feature_name ], + sh:order 26 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 45 ; - sh:path biolink:has_supporting_studies ], + sh:order 39 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:order 51 ; + sh:path biolink:id ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:object_specialization_qualifier ], + sh:order 49 ; + sh:path biolink:evidence_count ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 24 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 55 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_closure ], + sh:order 6 ; + sh:path biolink:object_specialization_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:original_predicate ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 56 ; - sh:path dct:description ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 31 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_closure ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], + sh:order 35 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_feature_name ], + sh:order 20 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:order 21 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 42 ; + sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:has_adverse_event ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:subject_specialization_qualifier ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:has_confidence_score ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 57 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 56 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:subject_namespace ], + sh:order 50 ; + sh:path biolink:semmed_agreement_count ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path rdf:type ], + sh:order 46 ; + sh:path biolink:update_date ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 45 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 58 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:subject_category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:original_object ], + sh:order 32 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 57 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 5 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:evidence_count ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentAdverseEventAssociation . - -biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an unintended, but predictable, secondary effect of the treatment." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 30 ; + sh:path biolink:object_feature_name ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:negated ], + sh:order 59 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path dct:description ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 33 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:semmed_agreement_count ], + sh:order 47 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 54 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 18 ; sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:object_closure ], + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 58 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; sh:order 9 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 10 ; sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path biolink:subject_label_closure ], + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:subject_closure ], + sh:order 29 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:order 36 ; + sh:path biolink:object_category_closure ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentAdverseEventAssociation . + +biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation a sh:NodeShape ; + rdfs:comment "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an unintended, but predictable, secondary effect of the treatment." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:sources ], + sh:order 57 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:original_object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 23 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 37 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:qualifiers ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:adjusted_p_value ], + sh:order 8 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 51 ; + sh:path biolink:iri ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9960,23 +9952,6 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_feature_name ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -9984,57 +9959,33 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 22 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:subject_namespace ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 44 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:publications ], + sh:order 42 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 33 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 56 ; - sh:path biolink:has_attribute ], + sh:order 24 ; + sh:path biolink:timepoint ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; @@ -10046,56 +9997,42 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 45 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:category ], + sh:order 48 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:object_label_closure ], + sh:order 27 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 55 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:elevate_to_prediction ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 54 ; + sh:path rdfs:label ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; @@ -10103,68 +10040,27 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation a sh:NodeShape ; sh:order 58 ; sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:object_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_evidence ], + sh:order 36 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:deprecated ], + sh:order 35 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:subject_category_closure ], + sh:order 43 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -10172,158 +10068,260 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_specialization_qualifier ], + sh:order 4 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:category ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:iri ], + sh:order 26 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:sources ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 56 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:subject_specialization_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 12 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation . - -biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the chemical or treatment is used to treat, or is being studied to treat, the disease or phenotypic feature." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 47 ; + sh:path biolink:elevate_to_prediction ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:object_category_closure ], + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:has_side_effect ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 58 ; - sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:sources ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 22 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 23 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:object_feature_name ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path biolink:subject_label_closure ], + sh:path biolink:subject_label_closure ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectAssociation . + +biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the chemical or treatment is used to treat, or is being studied to treat, the disease or phenotypic feature." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 54 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:qualified_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_confidence_score ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 47 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:subject_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -10331,28 +10329,41 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:order 51 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:qualifier ], + sh:order 29 ; + sh:path biolink:object_feature_name ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:negated ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:object_specialization_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:ameliorates_condition biolink:applied_to_treat biolink:beneficial_in_models_for biolink:in_clinical_trials_for biolink:in_preclinical_trials_for biolink:preventative_for_condition biolink:studied_to_treat biolink:treats biolink:treats_or_applied_or_studied_to_treat ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:retrieval_source_ids ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; @@ -10360,216 +10371,245 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:order 48 ; sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 38 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 46 ; + sh:path biolink:has_confidence_score ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path rdf:type ], + sh:order 24 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 22 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:negated ], + sh:order 33 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 44 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 50 ; + sh:path biolink:id ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 23 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 45 ; + sh:path biolink:update_date ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 17 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 56 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:original_subject ], + sh:order 26 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 55 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 52 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:deprecated ], + sh:order 58 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:has_evidence ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 56 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:order 35 ; + sh:path biolink:object_category_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:subject_specialization_qualifier ], + sh:order 13 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:sources ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_feature_name ], + sh:order 19 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 57 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path rdfs:label ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 37 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 23 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:subject_closure ] ; + sh:order 42 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; + rdfs:comment "An interaction between a chemical entity and another entity" ; sh:closed false ; - sh:description "An interaction between a chemical entity and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -10580,138 +10620,168 @@ biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; sh:targetClass biolink:ChemicalToEntityAssociationMixin . biolink:ChiSquaredAnalysisResult a sh:NodeShape ; + rdfs:comment "A result of a chi squared analysis." ; sh:closed true ; - sh:description "A result of a chi squared analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ] ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:ChiSquaredAnalysisResult . biolink:ClinicalCourse a sh:NodeShape ; + rdfs:comment "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; sh:closed true ; - sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -10719,56 +10789,28 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -10778,44 +10820,53 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:targetClass biolink:ClinicalCourse . biolink:ClinicalEntity a sh:NodeShape ; + rdfs:comment "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; sh:closed true ; - sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -10823,101 +10874,86 @@ biolink:ClinicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ] ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ClinicalEntity . biolink:ClinicalFinding a sh:NodeShape ; + rdfs:comment "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:closed true ; - sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], [ sh:class biolink:GeneticInheritance ; sh:description "Connects genetic inheritance to a disease or phenotypic feature, as a node property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:inheritance ], - [ sh:class biolink:ClinicalAttribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -10925,36 +10961,29 @@ biolink:ClinicalFinding a sh:NodeShape ; sh:order 14 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:information_content ], + sh:order 12 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -10962,52 +10991,60 @@ biolink:ClinicalFinding a sh:NodeShape ; sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:class biolink:ClinicalAttribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:equivalent_identifiers ] ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ] ; sh:targetClass biolink:ClinicalFinding . biolink:ClinicalMeasurement a sh:NodeShape ; + rdfs:comment "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; sh:closed true ; - sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 15 ; + sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -11015,95 +11052,114 @@ biolink:ClinicalMeasurement a sh:NodeShape ; sh:order 12 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:information_content ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], + sh:order 13 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ClinicalMeasurement . biolink:ClinicalModifier a sh:NodeShape ; + rdfs:comment "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; sh:closed true ; - sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; @@ -11111,48 +11167,51 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:order 11 ; sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -11160,401 +11219,376 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ] ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:ClinicalModifier . biolink:ClinicalTrial a sh:NodeShape ; + rdfs:comment "A clinical trial is a research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes." ; sh:closed true ; - sh:description "A clinical trial is a research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:date ; + sh:property [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:creation_date ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects a clinical trial to one or more conditions being studied in the trial" ; + [ sh:class biolink:StudyResult ; + sh:description "Connects an study to instances of its study result" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:clinical_trial_conditions ], + sh:order 14 ; + sh:path biolink:has_study_results ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:iri ], + [ sh:description "The phase that a clinical trials study represents" ; + sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_1_to_2" "clinical_trial_phase_2" "clinical_trial_phase_2_to_3" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_trial_phase ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Records whether the clinical trials are testing the intervention." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path biolink:clinical_trial_tested_intervention ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:id ], - [ sh:class biolink:ClinicalIntervention ; - sh:description "connects a clinical trial to one or more interventions being tested in the trial" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:clinical_trial_interventions ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:order 25 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:taxon ], + sh:order 18 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:provided_by ], [ sh:description "The age stage of a clinical trial as determined by clinicaltrials.gov (adult, child, older adult)" ; sh:in ( "adult" "child" "older_adult" ) ; sh:order 8 ; sh:path biolink:clinical_trial_age_stage ], - [ sh:datatype xsd:string ; - sh:description "The start date of a clinical trial as determined by clinicaltrials.gov" ; + [ sh:description "The overall status of a clinical trial as determined by clinicaltrials.gov" ; + sh:in ( "ACTIVE_NOT_RECRUITING" "APPROVED_FOR_MARKETING" "AVAILABLE" "COMPLETED" "ENROLLING_BY_INVITATION" "NO_LONGER_AVAILABLE" "NOT_YET_RECRUITING" "RECRUITING" "SUSPENDED" "TEMPORARILY_NOT_AVAILABLE" "TERMINATED" "UNKNOWN" "WITHDRAWN" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:clinical_trial_start_date ], - [ sh:datatype xsd:string ; - sh:description "The enrollment type of a clinical trial as determined by clinicaltrials.gov (actual, anticipated, or estimated)" ; + sh:order 3 ; + sh:path biolink:clinical_trial_overall_status ], + [ sh:datatype xsd:integer ; + sh:description "The enrollment number of a clinical trial as determined by clinicaltrials.gov" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:clinical_trial_enrollment_type ], + sh:order 7 ; + sh:path biolink:clinical_trial_enrollment ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The brief title of a clinical trial as determined by clinicaltrials.gov" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:clinical_trial_brief_title ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:equivalent_identifiers ], - [ sh:description "The phase that a clinical trials study represents" ; - sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_1_to_2" "clinical_trial_phase_2" "clinical_trial_phase_2_to_3" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_trial_phase ], + [ sh:class biolink:ClinicalIntervention ; + sh:description "connects a clinical trial to one or more interventions being tested in the trial" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:clinical_trial_interventions ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The intervention model of a clinical trial as determined by clinicaltrials.gov. The most common values are SINGLE_GROUP, PARALLEL, CROSSOVER, FACTORIAL, and (null)." ; + sh:description "The enrollment type of a clinical trial as determined by clinicaltrials.gov (actual, anticipated, or estimated)" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:clinical_trial_intervention_model ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:clinical_trial_enrollment_type ], [ sh:datatype xsd:string ; - sh:description "The brief title of a clinical trial as determined by clinicaltrials.gov" ; + sh:description "The age range of a clinical trial as determined by clinicaltrials.gov" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:clinical_trial_brief_title ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 9 ; + sh:path biolink:clinical_trial_age_range ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:information_content ], + sh:order 22 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:xref ], - [ sh:datatype xsd:integer ; - sh:description "The enrollment number of a clinical trial as determined by clinicaltrials.gov" ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects a clinical trial to one or more conditions being studied in the trial" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:clinical_trial_conditions ], + [ sh:datatype xsd:string ; + sh:description "The intervention model of a clinical trial as determined by clinicaltrials.gov. The most common values are SINGLE_GROUP, PARALLEL, CROSSOVER, FACTORIAL, and (null)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:clinical_trial_enrollment ], + sh:order 2 ; + sh:path biolink:clinical_trial_intervention_model ], [ sh:datatype xsd:string ; - sh:description "Records whether the clinical trials are testing the intervention." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:clinical_trial_tested_intervention ], - [ sh:class biolink:StudyResult ; - sh:description "Connects an study to instances of its study result" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_study_results ], + sh:order 17 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The age range of a clinical trial as determined by clinicaltrials.gov" ; + sh:description "The primary purpose of a clinical trial as determined by clinicaltrials.gov. The most common values are TREATMENT and PREVENTION. Other possible values include BASIC_SCIENCE, SUPPORTIVE_CARE, DIAGNOSTIC, HEALTH_SERVICES_RESEARCH, SCREENING, DEVICE_FEASIBILITY, OTHER, and (null)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:clinical_trial_age_range ], + sh:order 1 ; + sh:path biolink:clinical_trial_primary_purpose ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:deprecated ], - [ sh:description "The overall status of a clinical trial as determined by clinicaltrials.gov" ; - sh:in ( "ACTIVE_NOT_RECRUITING" "APPROVED_FOR_MARKETING" "AVAILABLE" "COMPLETED" "ENROLLING_BY_INVITATION" "NO_LONGER_AVAILABLE" "NOT_YET_RECRUITING" "RECRUITING" "SUSPENDED" "TEMPORARILY_NOT_AVAILABLE" "TERMINATED" "UNKNOWN" "WITHDRAWN" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:clinical_trial_overall_status ], [ sh:datatype xsd:string ; - sh:description "The primary purpose of a clinical trial as determined by clinicaltrials.gov. The most common values are TREATMENT and PREVENTION. Other possible values include BASIC_SCIENCE, SUPPORTIVE_CARE, DIAGNOSTIC, HEALTH_SERVICES_RESEARCH, SCREENING, DEVICE_FEASIBILITY, OTHER, and (null)." ; + sh:description "The start date of a clinical trial as determined by clinicaltrials.gov" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:clinical_trial_primary_purpose ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 6 ; + sh:path biolink:clinical_trial_start_date ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:full_name ] ; + sh:order 21 ; + sh:path biolink:taxon ] ; sh:targetClass biolink:ClinicalTrial . biolink:CodingSequence a sh:NodeShape ; + rdfs:comment "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:information_content ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:information_content ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:order 10 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ] ; sh:targetClass biolink:CodingSequence . biolink:Cohort a sh:NodeShape ; + rdfs:comment "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; sh:closed true ; - sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -11562,25 +11596,35 @@ biolink:Cohort a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:taxon ] ; sh:targetClass biolink:Cohort . biolink:CommonDataElement a sh:NodeShape ; + rdfs:comment "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; sh:closed true ; - sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -11588,17 +11632,27 @@ biolink:CommonDataElement a sh:NodeShape ; sh:order 11 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 9 ; + sh:path biolink:information_content ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -11606,103 +11660,108 @@ biolink:CommonDataElement a sh:NodeShape ; sh:order 18 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 12 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 15 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:information_content ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ] ; + sh:path biolink:taxon ] ; sh:targetClass biolink:CommonDataElement . biolink:ComplexChemicalExposure a sh:NodeShape ; + rdfs:comment "A complex chemical exposure is an intake of a chemical mixture, other than a drug." ; sh:closed true ; - sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:exposure_end_age ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -11710,44 +11769,47 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; sh:order 20 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:exposure_magnitude ], + sh:order 8 ; + sh:path biolink:exposure_additional_condition ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Route of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 3 ; + sh:path biolink:exposure_route ], [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:exposure_type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:exposure_magnitude ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; + sh:order 15 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_end_age ], + sh:order 16 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:order 21 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Type of exposure" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], + sh:order 1 ; + sh:path biolink:exposure_type ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -11755,130 +11817,117 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; sh:order 0 ; sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:exposure_route ], - [ sh:datatype xsd:string ; - sh:description "Type of an exposure event." ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:exposure_vehicle ], + sh:order 11 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:taxon ], + sh:order 23 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:time ; sh:description "Duration of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:exposure_duration ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path rdf:type ], [ sh:datatype xsd:integer ; sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; + sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:exposure_additional_condition ] ; + sh:order 2 ; + sh:path biolink:exposure_vehicle ] ; sh:targetClass biolink:ComplexChemicalExposure . biolink:ComplexMolecularMixture a sh:NodeShape ; + rdfs:comment "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:closed true ; - sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:equivalent_identifiers ], + sh:order 24 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:has_attribute ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path rdf:type ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; + sh:order 9 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "Tern indicating the chirality of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 14 ; + sh:path biolink:chembl_chirality ], [ sh:datatype xsd:boolean ; sh:description "Flag indicating if a chemical entity is a natural product." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:chembl_natural_product ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:xref ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; - sh:order 9 ; - sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -11886,51 +11935,73 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:order 22 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "Text indicating the availability type of the chemical entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:chembl_availability_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 27 ; + sh:path dct:description ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; - sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:chembl_black_box_warning ], + sh:order 3 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:order 26 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], + sh:order 18 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Text indicating the availability type of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:chembl_availability_type ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:chembl_drug_warning ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; sh:maxCount 1 ; @@ -11938,71 +12009,86 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:order 10 ; sh:path biolink:chembl_prodrug ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path rdfs:label ], + sh:order 25 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 23 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; + sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:chembl_black_box_warning ] ; + sh:targetClass biolink:ComplexMolecularMixture . + +biolink:ConceptCountAnalysisResult a sh:NodeShape ; + rdfs:comment "A result of a concept count analysis." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:order 7 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:chembl_drug_warning ], + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 5 ; sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; + sh:order 9 ; sh:path biolink:category ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "Tern indicating the chirality of the chemical entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:chembl_chirality ] ; - sh:targetClass biolink:ComplexMolecularMixture . - -biolink:ConceptCountAnalysisResult a sh:NodeShape ; - sh:closed true ; - sh:description "A result of a concept count analysis." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -12019,123 +12105,101 @@ biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ] ; + sh:order 4 ; + sh:path biolink:equivalent_identifiers ] ; sh:targetClass biolink:ConceptCountAnalysisResult . biolink:ConfidenceLevel a sh:NodeShape ; + rdfs:comment "Level of confidence in a statement" ; sh:closed true ; - sh:description "Level of confidence in a statement" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; @@ -12143,47 +12207,44 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:order 9 ; sh:path biolink:information_content ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -12192,166 +12253,203 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:order 11 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:order 16 ; + sh:path dct:description ] ; sh:targetClass biolink:ConfidenceLevel . biolink:ContributorAssociation a sh:NodeShape ; + rdfs:comment "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:closed true ; - sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Agent ; - sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:evidence_count ], + [ sh:datatype xsd:anyURI ; + sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:in ( biolink:author biolink:contributor biolink:editor biolink:provider biolink:publisher ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; - sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Agent ; + sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 46 ; + sh:path dct:description ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:InformationContentEntity ; sh:description "information content entity which an agent has helped realise" ; sh:maxCount 1 ; @@ -12359,45 +12457,50 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -12405,94 +12508,54 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:order 16 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + [ sh:class biolink:OntologyClass ; + sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ] ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:ContributorAssociation . biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association between a gene (or gene product) and a disease for which the gene is statistically correlated with the disease rather than asserted as causal. Such associations typically derive from GWAS, co-occurrence analyses, or other statistical methods, and are annotated with scores such as a z-score or a diseases confidence score." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:qualifiers ], + sh:order 13 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -12500,188 +12563,184 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_evidence ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:knowledge_level ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 56 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 2 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:category ], + sh:order 45 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path biolink:subject_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_closure ], + sh:order 59 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:subject_category ], + sh:order 29 ; + sh:path biolink:object_category ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 21 ; - sh:path biolink:agent_type ], + sh:order 26 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:qualifier ], + sh:order 22 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:original_predicate ], + sh:order 6 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 58 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:timepoint ], + sh:order 55 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 54 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:biomarker_for biolink:coexpressed_with biolink:correlated_with biolink:has_biomarker biolink:negatively_correlated_with biolink:occurs_together_in_literature_with biolink:positively_correlated_with ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:object_category_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 59 ; - sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 51 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualified_predicate ], + sh:order 19 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value." ; + sh:order 31 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:z_score ], + sh:order 43 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to correlate with the disease." ; + sh:order 27 ; + sh:path biolink:object_feature_name ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 7 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 57 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:negated ], + sh:order 24 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_evidence_of_type ], + sh:order 14 ; + sh:path biolink:sources ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -12689,6 +12748,24 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to correlate with the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 7 ; + sh:path rdf:subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:float ; sh:description "A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale." ; sh:maxCount 1 ; @@ -12696,403 +12773,395 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:order 1 ; sh:path biolink:diseases_confidence_score ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 36 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:subject_form_or_variant_qualifier ], + sh:order 18 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 56 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:supporting_text ], + sh:order 48 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 49 ; sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 54 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 52 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdf:predicate ], + sh:order 35 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 5 ; + sh:path biolink:allelic_requirement ; + sh:pattern "^HP:\\d{7}$" ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:object_label_closure ], + sh:order 10 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 53 ; sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:sources ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_feature_name ], + sh:order 44 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:allelic_requirement ; - sh:pattern "^HP:\\d{7}$" ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 11 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 58 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 21 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_supporting_studies ] ; + sh:order 0 ; + sh:path biolink:z_score ] ; sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . biolink:DatasetSummary a sh:NodeShape ; + rdfs:comment "an item that holds summary level information about a dataset." ; sh:closed true ; - sh:description "an item that holds summary level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:license ], + sh:order 18 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:format ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path schema1:logo ], - [ sh:datatype xsd:string ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:source_web_page ], + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A URL referencing an image that serves as the visual logo of a data source." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], + sh:order 1 ; + sh:path schema1:logo ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 13 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A URL of a web page that documents or serves as the landing page for a data source." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], + sh:order 0 ; + sh:path biolink:source_web_page ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:license ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:rights ] ; + sh:path biolink:information_content ] ; sh:targetClass biolink:DatasetSummary . biolink:DatasetVersion a sh:NodeShape ; + rdfs:comment "an item that holds version level information about a dataset." ; sh:closed true ; - sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:class biolink:DatasetDistribution ; + sh:description "The date on which a dataset version was ingested into the local knowledge graph or downstream data system; a specialization of dct:issued for the ingestion context." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path dct:distribution ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:order 1 ; + sh:path biolink:ingest_date ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:equivalent_identifiers ], + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:format ], + sh:order 13 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 11 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:taxon ], + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:ingest_date ], + sh:order 18 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:Dataset ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_dataset ], + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + [ sh:class biolink:DatasetDistribution ; + sh:description "Links a dataset version to one of its dataset distributions (a specific representation or serialization of the dataset)." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path dct:distribution ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:class biolink:Dataset ; + sh:description "Links a dataset version to the underlying dataset that it is a version of." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ] ; + sh:order 0 ; + sh:path biolink:has_dataset ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:DatasetVersion . biolink:DiagnosticAid a sh:NodeShape ; + rdfs:comment "A device or substance used to help diagnose disease or injury" ; sh:closed true ; - sh:description "A device or substance used to help diagnose disease or injury" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -13104,23 +13173,6 @@ biolink:DiagnosticAid a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -13131,239 +13183,239 @@ biolink:DiagnosticAid a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ] ; + sh:order 7 ; + sh:path biolink:id ] ; sh:targetClass biolink:DiagnosticAid . biolink:DiseaseAssociatedWithResponseToChemicalEntityAssociation a sh:NodeShape ; + rdfs:comment "A statistical association between a disease and a chemical entity where the chemical entity has a therapeutic or adverse effect on the disease progression, symptoms or outcomes in a patient, cell line, or any model system." ; sh:closed true ; - sh:description "A statistical association between a disease and a chemical entity where the chemical entity has a therapeutic or adverse effect on the disease progression, symptoms or outcomes in a patient, cell line, or any model system." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:elevate_to_prediction ], - [ sh:description "a biological response (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:in ( "therapeutic_response" "negative" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:response_context_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category ], + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 30 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 42 ; + sh:path biolink:semmed_agreement_count ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 47 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path dct:description ], + sh:order 50 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_namespace ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_closure ], + sh:order 49 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:supporting_text ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 9 ; + sh:path biolink:sources ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:update_date ], + sh:order 48 ; + sh:path dct:description ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -13371,188 +13423,249 @@ biolink:DiseaseAssociatedWithResponseToChemicalEntityAssociation a sh:NodeShape sh:order 15 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Disease ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 43 ; + sh:path biolink:id ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 41 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 39 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:associated_with_resistance_to biolink:associated_with_response_to biolink:associated_with_sensitivity_to ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:p_value ], + [ sh:description "a biological response target (a patient, a cohort, a model system, a cell line, a sample of biological material, etc.)" ; + sh:in ( "cohort" "cell line" "individual" "sample" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:response_target_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:id ], + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:semmed_agreement_count ], - [ sh:description "a biological response target (a patient, a cohort, a model system, a cell line, a sample of biological material, etc.)" ; - sh:in ( "cohort" "cell line" "individual" "sample" ) ; + sh:order 25 ; + sh:path biolink:subject_closure ], + [ sh:description "a biological response (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:in ( "therapeutic_response" "negative" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:response_target_context_qualifier ], + sh:order 0 ; + sh:path biolink:response_context_qualifier ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:deprecated ], + sh:order 40 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:sources ] ; + sh:order 21 ; + sh:path biolink:subject_feature_name ] ; sh:targetClass biolink:DiseaseAssociatedWithResponseToChemicalEntityAssociation . biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; + rdfs:comment "A disease or phenotypic feature state, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome,." ; sh:closed true ; - sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:description "Route of exposure." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], + sh:order 3 ; + sh:path biolink:exposure_route ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:order 17 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:exposure_magnitude ], + sh:order 16 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:exposure_vehicle ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:taxon ], + sh:order 8 ; + sh:path biolink:exposure_additional_condition ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:exposure_magnitude ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:category ], + [ sh:datatype xsd:integer ; + sh:description "Starting age of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:exposure_start_age ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:full_name ], - [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_end_age ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 23 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:exposure_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:exposure_additional_condition ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], + sh:order 5 ; + sh:path biolink:exposure_end_age ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -13560,81 +13673,46 @@ biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:order 20 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:exposure_route ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], + sh:order 19 ; + sh:path rdf:type ], [ sh:datatype xsd:time ; sh:description "Duration of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:exposure_duration ], - [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ] ; + sh:order 10 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; + rdfs:comment "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." ; sh:closed true ; - sh:description "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureOutcome . biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13645,399 +13723,411 @@ biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape ; + rdfs:comment "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; sh:closed true ; - sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 44 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:GeneticInheritance ; - sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:GeneticInheritance ; + sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:has_mode_of_inheritance ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; + sh:path biolink:publications ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + +biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; + rdfs:comment "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . - -biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 41 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -14045,26 +14135,23 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:order 42 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -14072,23 +14159,39 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:order 48 ; sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:class biolink:AnatomicalEntity ; sh:description "anatomical entity in which the disease or feature is found." ; sh:maxCount 1 ; @@ -14096,17 +14199,22 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -14114,87 +14222,40 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:order 36 ; sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -14203,20 +14264,39 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ] ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; + rdfs:comment "A mixin applied to any association whose subject (source node) is a disease." ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:NamedThing ; @@ -14226,144 +14306,158 @@ biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:DiseaseToEntityAssociationMixin . biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; + rdfs:comment "An association between an exposure event and a disease." ; sh:closed true ; - sh:description "An association between an exposure event and a disease." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -14371,74 +14465,66 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:evidence_count ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -14446,122 +14532,119 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ] ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:DiseaseToExposureEventAssociation . biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; sh:closed true ; - sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 60 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_feature_name ], + sh:order 49 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 53 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 2 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:original_object ], + sh:order 42 ; + sh:path biolink:update_date ], [ sh:class biolink:Disease ; sh:description "disease class" ; sh:maxCount 1 ; @@ -14569,331 +14652,358 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path rdf:subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:qualifiers ], + sh:order 39 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:update_date ], + sh:order 47 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path dct:description ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 25 ; + sh:path biolink:subject_feature_name ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdf:predicate ], + sh:order 57 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 61 ; sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path rdf:type ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:has_count ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 59 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_evidence_of_type ], + sh:order 13 ; + sh:path biolink:sources ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path rdf:type ], + sh:order 36 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:object_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 58 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 29 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_percentage ], + sh:order 22 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:object_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 56 ; - sh:path biolink:subject_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:iri ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; sh:order 55 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:retrieval_source_ids ], + sh:order 11 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 31 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:semmed_agreement_count ], + sh:order 26 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_percentage ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:onset_qualifier ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_quotient ], + sh:order 44 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 56 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 59 ; - sh:path biolink:qualified_predicate ], + sh:order 54 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:qualifier ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:sources ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 43 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 45 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 53 ; - sh:path biolink:has_attribute ], + sh:order 41 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_namespace ], + sh:order 52 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 21 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 60 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_predicate ], + sh:order 51 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 33 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 6 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . + +biolink:DrugExposure a sh:NodeShape ; + rdfs:comment "A drug exposure is an intake of a particular drug." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type biolink:has_gene_or_gene_product ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_confidence_score ], + sh:order 2 ; + sh:path biolink:exposure_type ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_evidence ], + sh:order 21 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_total ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 58 ; - sh:path biolink:object_direction_qualifier ] ; - sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . - -biolink:DrugExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A drug exposure is an intake of a particular drug." ; - sh:ignoredProperties ( biolink:has_gene_or_gene_product rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 14 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -14905,23 +15015,39 @@ biolink:DrugExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:iri ], + [ sh:datatype xsd:integer ; + sh:description "Starting age of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:exposure_start_age ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:exposure_duration ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -14929,17 +15055,11 @@ biolink:DrugExposure a sh:NodeShape ; sh:order 22 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:exposure_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], + sh:order 13 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Route of exposure." ; sh:maxCount 1 ; @@ -14952,72 +15072,18 @@ biolink:DrugExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:xref ], - [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:exposure_magnitude ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:exposure_duration ], [ sh:datatype xsd:string ; sh:description "Type of an exposure event." ; sh:maxCount 1 ; @@ -15030,6 +15096,19 @@ biolink:DrugExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:exposure_end_age ], + [ sh:datatype xsd:string ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:exposure_magnitude ], + [ sh:datatype xsd:string ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -15039,101 +15118,120 @@ biolink:DrugExposure a sh:NodeShape ; sh:targetClass biolink:DrugExposure . biolink:DrugLabel a sh:NodeShape ; + rdfs:comment "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; sh:closed true ; - sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 22 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], + sh:order 17 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path dct:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 21 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 20 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -15141,17 +15239,17 @@ biolink:DrugLabel a sh:NodeShape ; sh:order 16 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + sh:order 18 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; @@ -15159,46 +15257,31 @@ biolink:DrugLabel a sh:NodeShape ; sh:order 15 ; sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ] ; + sh:order 2 ; + sh:path biolink:summary ] ; sh:targetClass biolink:DrugLabel . biolink:DrugToEntityAssociationMixin a sh:NodeShape ; + rdfs:comment "An interaction between a drug and another entity" ; sh:closed false ; - sh:description "An interaction between a drug and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:Drug ; + sh:description "the drug that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -15209,137 +15292,117 @@ biolink:DrugToEntityAssociationMixin a sh:NodeShape ; sh:targetClass biolink:DrugToEntityAssociationMixin . biolink:DrugToGeneAssociation a sh:NodeShape ; + rdfs:comment "An interaction between a drug and a gene or gene product." ; sh:closed true ; - sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product that is affected by the drug" ; + sh:order 46 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], [ sh:class biolink:Drug ; sh:description "the drug that is an interactor" ; sh:maxCount 1 ; @@ -15347,204 +15410,222 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product that is affected by the drug" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ] ; - sh:targetClass biolink:DrugToGeneAssociation . - -biolink:DrugToGeneInteractionExposure a sh:NodeShape ; - sh:closed true ; - sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:full_name ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; + sh:order 42 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:exposure_type ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:exposure_start_age ], + sh:path biolink:publications ] ; + sh:targetClass biolink:DrugToGeneAssociation . + +biolink:DrugToGeneInteractionExposure a sh:NodeShape ; + rdfs:comment "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:time ; sh:description "Duration of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:exposure_duration ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:timepoint ], + sh:order 4 ; + sh:path biolink:exposure_vehicle ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -15552,83 +15633,85 @@ biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:order 23 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:exposure_additional_condition ], + [ sh:datatype xsd:string ; + sh:description "Route of exposure." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:xref ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 5 ; + sh:path biolink:exposure_route ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:information_content ], + sh:order 14 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:taxon ], + sh:order 9 ; + sh:path biolink:exposure_magnitude ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 15 ; + sh:path biolink:synonym ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:equivalent_identifiers ], + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:exposure_magnitude ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 3 ; + sh:path biolink:exposure_type ], + [ sh:datatype xsd:integer ; + sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path biolink:has_quantitative_value ], + sh:order 6 ; + sh:path biolink:exposure_start_age ], [ sh:datatype xsd:integer ; sh:description "Ending stage of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:exposure_end_age ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_route ], - [ sh:datatype xsd:string ; - sh:description "Type of an exposure event." ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:exposure_vehicle ], + sh:order 17 ; + sh:path biolink:information_content ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -15636,345 +15719,340 @@ biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:order 25 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:exposure_additional_condition ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ] ; + sh:order 22 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:taxon ] ; sh:targetClass biolink:DrugToGeneInteractionExposure . biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association between a gene (or gene product) and a disease in which the gene is classified by its druggability (e.g., via the IDG/Pharos target development-level tiers)." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:object_closure ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 55 ; + sh:path biolink:has_attribute ], + [ sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( "biolink:contributes_to" "biolink:associated_with" ), + ( "target_for" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "Classification of druggable genes based on knowledge about drug or small molecule activities." ; + sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:druggable_gene_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 57 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 47 ; sh:path biolink:evidence_count ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:semmed_agreement_count ], + sh:order 51 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 37 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum). See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:gene2phenotype_confidence_category ], + sh:order 24 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path dct:description ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 28 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; sh:maxCount 1 ; - sh:order 57 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:allelic_requirement ; + sh:pattern "^HP:\\d{7}$" ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:diseases_confidence_score ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:subject_label_closure ], + sh:order 31 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 22 ; + sh:path biolink:agent_type ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 58 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 43 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 54 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_evidence_of_type ], + sh:order 34 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_feature_name ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:sources ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:adjusted_p_value ], + sh:order 49 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 58 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:negated ], + sh:order 8 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:qualifier ], + sh:order 23 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum). See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:gene2phenotype_confidence_category ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 59 ; sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 43 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:publications ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 56 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:category ], - [ sh:description "Classification of druggable genes based on knowledge about drug or small molecule activities." ; - sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:druggable_gene_category ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_confidence_score ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 22 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:allelic_requirement ; - sh:pattern "^HP:\\d{7}$" ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:original_object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 48 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:original_subject ], + sh:order 12 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:qualifiers ], + sh:order 42 ; + sh:path biolink:supporting_text ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 60 ; sh:path biolink:frequency_qualifier ], - [ sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:in ( "biolink:contributes_to" "biolink:associated_with" ) ; + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_closure ], + sh:order 56 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:subject_namespace ], + sh:order 52 ; + sh:path rdf:type ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 21 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:diseases_confidence_score ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 55 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualified_predicate ], + sh:order 29 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:supporting_text ], + sh:order 35 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -15987,38 +16065,81 @@ biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_closure ] ; + sh:order 20 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:p_value ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ] ; sh:targetClass biolink:DruggableGeneToDiseaseAssociation . biolink:Edge a sh:NodeShape ; + rdfs:comment "A generic edge in a KGX-formatted knowledge graph, representing a directed relationship between a subject node and an object node qualified by a predicate. This class serves as the structural superclass for `association` in Biolink, providing the minimal KGX-compliant contract (subject, predicate, object, and associated metadata) that any biolink relationship participating in a knowledge graph must satisfy." ; sh:closed true ; - sh:description "An edge in a KGX graph, will be superclass for association" ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:Edge . biolink:EntityToDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association between any entity and a disease, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:supporting_text ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:sources ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 51 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Numbers that identify specific drug applications. Each drug can have multiple approval numbers (for example, as seen with ranitidine having both ANADA200536 and ANDA200536)." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:FDA_regulatory_approvals ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -16031,307 +16152,281 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:integer ; + sh:description "The number of cases in a study or clinical trial, primarily used in conversion of drug approval data." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:number_of_cases ], + [ sh:description "The maximum research phase reached for a specific chemical-disease pair, indicating the highest clinical trial phase achieved for the chemical entity's investigation as a treatment for the associated disease or condition." ; + sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_1_to_2" "clinical_trial_phase_2" "clinical_trial_phase_2_to_3" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:max_research_phase ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], + sh:order 6 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], + sh:order 19 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 17 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_confidence_score ], - [ sh:description "The maximum research phase reached for a specific chemical-disease pair, indicating the highest clinical trial phase achieved for the chemical entity's investigation as a treatment for the associated disease or condition." ; - sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_1_to_2" "clinical_trial_phase_2" "clinical_trial_phase_2_to_3" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_attribute ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 18 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:datatype xsd:integer ; - sh:description "The number of cases in a study or clinical trial, primarily used in conversion of drug approval data." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:number_of_cases ], + sh:order 23 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 48 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:deprecated ], + sh:order 45 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], + sh:order 34 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 49 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path dct:description ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:description "The clinical approval status of a chemical entity for treating a specific disease or condition, as captured in the context of the association between the chemical and the disease." ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 31 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_supporting_studies ], + sh:order 30 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Numbers that identify specific drug applications. Each drug can have multiple approval numbers (for example, as seen with ranitidine having both ANADA200536 and ANDA200536)." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:FDA_regulatory_approvals ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], + sh:order 4 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:evidence_count ], + sh:order 27 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], + sh:order 14 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 29 ; + sh:path biolink:subject_category_closure ], + [ sh:description "The clinical approval status of a chemical entity for treating a specific disease or condition, as captured in the context of the association between the chemical and the disease." ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 20 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 24 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:timepoint ] ; + sh:order 50 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_confidence_score ] ; sh:targetClass biolink:EntityToDiseaseAssociation . biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; + rdfs:comment "mixin class for any association whose object (target node) is a disease" ; sh:closed false ; - sh:description "mixin class for any association whose object (target node) is a disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:subject ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -16339,44 +16434,33 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:frequency_qualifier ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; sh:order 2 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdf:predicate ] ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ] ; sh:targetClass biolink:EntityToDiseaseAssociationMixin . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; @@ -16388,6 +16472,12 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:object_specialization_qualifier ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:disease_context_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -16395,13 +16485,6 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -16414,23 +16497,24 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:subject_specialization_qualifier ] ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; + rdfs:comment "An association between some entity and an exposure event." ; sh:closed false ; - sh:description "An association between some entity and an exposure event." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; @@ -16439,27 +16523,38 @@ biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:class biolink:ExposureEvent ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:EntityToExposureEventAssociationMixin . biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; + rdfs:comment "Qualifiers for entity to disease or phenotype associations." ; sh:closed false ; - sh:description "Qualifiers for entity to disease or phenotype associations." ; - sh:ignoredProperties ( biolink:has_total biolink:has_quotient rdf:type biolink:has_percentage biolink:sex_qualifier biolink:has_count ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:ignoredProperties ( biolink:has_count biolink:has_percentage biolink:has_total rdf:type biolink:sex_qualifier biolink:has_quotient ) ; + sh:property [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -16471,41 +16566,29 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:object_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:disease_context_qualifier ], + sh:order 9 ; + sh:path rdf:object ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -16513,30 +16596,23 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path rdf:object ] ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ] ; sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . biolink:EntityToFeatureOrGeneQualifiersMixin a sh:NodeShape ; + rdfs:comment "Qualifiers for entity to gene associations." ; sh:closed false ; - sh:description "Qualifiers for entity to gene associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -16544,11 +16620,12 @@ biolink:EntityToFeatureOrGeneQualifiersMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -16556,24 +16633,27 @@ biolink:EntityToFeatureOrGeneQualifiersMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -16584,34 +16664,20 @@ biolink:EntityToFeatureOrGeneQualifiersMixin a sh:NodeShape ; sh:targetClass biolink:EntityToFeatureOrGeneQualifiersMixin . biolink:EntityToFeatureOrVariantQualifiersMixin a sh:NodeShape ; + rdfs:comment "Qualifiers for entity to variant associations." ; sh:closed false ; - sh:description "Qualifiers for entity to variant associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:property [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 4 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -16619,36 +16685,55 @@ biolink:EntityToFeatureOrVariantQualifiersMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ] ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:EntityToFeatureOrVariantQualifiersMixin . biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; + rdfs:comment "An association between some entity and an outcome" ; sh:closed false ; - sh:description "An association between some entity and an outcome" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -16661,183 +16746,203 @@ biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:predicate ] ; sh:targetClass biolink:EntityToOutcomeAssociationMixin . biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "An association between any entity and a phenotypic feature, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 47 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:semmed_agreement_count ], + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Numbers that identify specific drug applications. Each drug can have multiple approval numbers (for example, as seen with ranitidine having both ANADA200536 and ANDA200536)." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:FDA_regulatory_approvals ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 23 ; + sh:path biolink:subject_feature_name ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 14 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:elevate_to_prediction ], + sh:order 22 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:negated ], + [ sh:description "The clinical approval status of a chemical entity for treating a specific disease or condition, as captured in the context of the association between the chemical and the disease." ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], + sh:order 40 ; + sh:path biolink:update_date ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:sources ], + sh:order 31 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 48 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 37 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:description "The clinical approval status of a chemical entity for treating a specific disease or condition, as captured in the context of the association between the chemical and the disease." ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 39 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 21 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:description "The maximum research phase reached for a specific chemical-disease pair, indicating the highest clinical trial phase achieved for the chemical entity's investigation as a treatment for the associated disease or condition." ; - sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_1_to_2" "clinical_trial_phase_2" "clinical_trial_phase_2_to_3" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], + sh:order 10 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:timepoint ], + sh:order 46 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], + sh:order 32 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 51 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -16845,153 +16950,128 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 49 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:category ], + sh:order 45 ; + sh:path biolink:id ], [ sh:datatype xsd:integer ; - sh:description "The number of cases in a study or clinical trial, primarily used in conversion of drug approval data." ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:number_of_cases ], + sh:order 43 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], + sh:order 20 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], + sh:order 36 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:supporting_text ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 41 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of cases in a study or clinical trial, primarily used in conversion of drug approval data." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_supporting_studies ], + sh:order 3 ; + sh:path biolink:number_of_cases ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The maximum research phase reached for a specific chemical-disease pair, indicating the highest clinical trial phase achieved for the chemical entity's investigation as a treatment for the associated disease or condition." ; + sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_1_to_2" "clinical_trial_phase_2" "clinical_trial_phase_2_to_3" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:max_research_phase ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; + sh:description "Numbers that identify specific drug applications. Each drug can have multiple approval numbers (for example, as seen with ranitidine having both ANADA200536 and ANDA200536)." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_confidence_score ], + sh:order 2 ; + sh:path biolink:FDA_regulatory_approvals ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 44 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:iri ] ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:subject ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; + rdfs:comment "A mixin applied to any association whose object (target node) is a phenotypic feature." ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:property [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 5 ; + sh:path biolink:has_total ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:disease_context_qualifier ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -16999,106 +17079,102 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:frequency_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:has_total ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:qualified_predicate ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:disease_context_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:has_count ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:frequency_qualifier ] ; + sh:path biolink:has_percentage ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . biolink:EnvironmentalExposure a sh:NodeShape ; + rdfs:comment "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; sh:closed true ; - sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:exposure_type ], + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -17106,164 +17182,173 @@ biolink:EnvironmentalExposure a sh:NodeShape ; sh:order 17 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 21 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:exposure_route ], + sh:order 20 ; + sh:path rdfs:label ], + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:exposure_end_age ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Route of exposure." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], + sh:order 3 ; + sh:path biolink:exposure_route ], [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; + sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_end_age ], + sh:order 4 ; + sh:path biolink:exposure_start_age ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:exposure_vehicle ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:exposure_magnitude ], + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:time ; sh:description "Duration of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:exposure_duration ], + [ sh:datatype xsd:string ; + sh:description "Type of exposure" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:exposure_type ], [ sh:datatype xsd:string ; sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:exposure_additional_condition ], + [ sh:datatype xsd:string ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:exposure_magnitude ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:path biolink:information_content ] ; + sh:targetClass biolink:EnvironmentalExposure . + +biolink:EnvironmentalFeature a sh:NodeShape ; + rdfs:comment "A system or entity in the natural environment that has the disposition to environ one or more material entities." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ] ; - sh:targetClass biolink:EnvironmentalExposure . - -biolink:EnvironmentalFeature a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -17271,98 +17356,98 @@ biolink:EnvironmentalFeature a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ] ; + sh:path biolink:synonym ] ; sh:targetClass biolink:EnvironmentalFeature . biolink:EnvironmentalFoodContaminant a sh:NodeShape ; + rdfs:comment "Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate foodstuffs during their production, transportation or storage." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "Text indicating the availability type of the chemical entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:chembl_availability_type ], - [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path biolink:chembl_drug_warning ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:equivalent_identifiers ], + sh:order 13 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; + sh:order 5 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:full_name ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:information_content ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:is_toxic ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:taxon ], + sh:order 19 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Tern indicating the chirality of the chemical entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:chembl_chirality ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -17370,123 +17455,104 @@ biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:order 23 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:chembl_black_box_warning ], + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:string ; + sh:description "Text indicating the availability type of the chemical entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:chembl_availability_type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:information_content ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:has_attribute ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; - sh:order 5 ; - sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a chemical entity is a natural product." ; + sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:chembl_natural_product ], + sh:order 6 ; + sh:path biolink:chembl_prodrug ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:synonym ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Tern indicating the chirality of the chemical entity." ; + sh:order 7 ; + sh:path biolink:chembl_black_box_warning ], + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a chemical entity is a natural product." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:chembl_chirality ], + sh:order 8 ; + sh:path biolink:chembl_natural_product ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:chembl_drug_warning ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:chembl_prodrug ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ] ; + sh:order 16 ; + sh:path biolink:equivalent_identifiers ] ; sh:targetClass biolink:EnvironmentalFoodContaminant . biolink:EnvironmentalProcess a sh:NodeShape ; + rdfs:comment "A process that occurs within or involves the components of an environmental system." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -17499,29 +17565,33 @@ biolink:EnvironmentalProcess a sh:NodeShape ; sh:order 4 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -17529,19 +17599,34 @@ biolink:EnvironmentalProcess a sh:NodeShape ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -17551,12 +17636,13 @@ biolink:EnvironmentalProcess a sh:NodeShape ; sh:targetClass biolink:EnvironmentalProcess . biolink:EpidemiologicalOutcome a sh:NodeShape ; + rdfs:comment "An epidemiological outcome, such as societal disease burden, resulting from an exposure event." ; sh:closed true ; - sh:description "An epidemiological outcome, such as societal disease burden, resulting from an exposure event." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:EpidemiologicalOutcome . biolink:EpigenomicEntity a sh:NodeShape ; + rdfs:comment "A mixin for entities that represent epigenomic modifications or features associated with heritable changes in gene expression that do not involve changes to the DNA sequence itself." ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; @@ -17568,15 +17654,15 @@ biolink:EpigenomicEntity a sh:NodeShape ; sh:targetClass biolink:EpigenomicEntity . biolink:Event a sh:NodeShape ; + rdfs:comment "Something that happens at a given place and time." ; sh:closed true ; - sh:description "Something that happens at a given place and time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -17584,33 +17670,17 @@ biolink:Event a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -17622,255 +17692,242 @@ biolink:Event a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Event . - -biolink:Evidence a sh:NodeShape ; - sh:closed true ; - sh:description "Dereferences detailed evidence that supports an association" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 2 ; sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 5 ; + sh:path biolink:information_content ] ; + sh:targetClass biolink:Event . + +biolink:Evidence a sh:NodeShape ; + rdfs:comment "Dereferences detailed evidence that supports an association" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 15 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 16 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 11 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:information_content ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:rights ] ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Evidence . biolink:ExonToTranscriptRelationship a sh:NodeShape ; + rdfs:comment "A transcript is formed from multiple exons" ; sh:closed true ; - sh:description "A transcript is formed from multiple exons" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:class biolink:Exon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Transcript ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -17878,350 +17935,472 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:Exon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ] ; + sh:order 19 ; + sh:path biolink:subject_feature_name ] ; sh:targetClass biolink:ExonToTranscriptRelationship . biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; + rdfs:comment "An association between an exposure event and an outcome." ; sh:closed true ; - sh:description "An association between an exposure event and an outcome." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category_closure ], + sh:order 21 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:category ], + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 0 ; + sh:path biolink:population_context_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:category ], + sh:order 25 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:has_confidence_score ], + sh:order 34 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path rdfs:label ], + sh:order 44 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 31 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_closure ], + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:update_date ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence_of_type ], + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_closure ], + sh:order 47 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_predicate ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:order 43 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 49 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], + sh:order 42 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_namespace ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:population_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:elevate_to_prediction ], + sh:order 26 ; + sh:path biolink:object_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 46 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 29 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:update_date ], + sh:order 40 ; + sh:path biolink:elevate_to_prediction ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -18229,512 +18408,404 @@ biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:order 16 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 10 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:adjusted_p_value ], + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:iri ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:evidence_count ], + sh:order 12 ; + sh:path biolink:knowledge_source ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:ExposureEventToOutcomeAssociation . + +biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 49 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:id ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:ExposureEventToOutcomeAssociation . - -biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], + sh:order 37 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:has_count ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 51 ; sh:path biolink:has_total ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 48 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:double ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], + sh:order 43 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 56 ; sh:path biolink:object_aspect_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 58 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 47 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 40 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 59 ; - sh:path biolink:disease_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 55 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 46 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 21 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], + sh:order 20 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sources ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 55 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdf:type ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; sh:order 54 ; sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 38 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 59 ; + sh:path biolink:disease_context_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 58 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 53 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 60 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 57 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:has_percentage ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ] ; + sh:order 17 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; + rdfs:comment "Qualifiers for disease or phenotype to entity associations." ; sh:closed false ; - sh:description "Qualifiers for disease or phenotype to entity associations." ; - sh:ignoredProperties ( biolink:has_total biolink:has_quotient rdf:type biolink:has_percentage biolink:sex_qualifier biolink:has_count ) ; - sh:property [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:anyURI ; + sh:ignoredProperties ( biolink:has_count biolink:has_percentage biolink:has_total rdf:type biolink:sex_qualifier biolink:has_quotient ) ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -18742,12 +18813,6 @@ biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -18755,118 +18820,112 @@ biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path rdf:object ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ] ; + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ] ; sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . biolink:Food a sh:NodeShape ; + rdfs:comment "A substance of plant, animal, or artificial origin consumed by a living organism to provide essential nutrients, energy, and support growth and the processes of life, or to satisfy other health needs or provide a social or organoleptic experience." ; sh:closed true ; - sh:description "A substance consumed by a living organism as a source of nutrition" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:chembl_prodrug ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 22 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a chemical entity is a natural product." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:chembl_natural_product ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:taxon ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:iri ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:full_name ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:description "Text indicating the availability type of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:chembl_drug_warning ], + sh:order 13 ; + sh:path biolink:chembl_availability_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:equivalent_identifiers ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -18874,126 +18933,163 @@ biolink:Food a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path rdf:type ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; - sh:order 9 ; - sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; sh:description "Tern indicating the chirality of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:chembl_chirality ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:full_name ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:chembl_black_box_warning ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a chemical entity is a natural product." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:xref ], + sh:order 12 ; + sh:path biolink:chembl_natural_product ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; + sh:order 9 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; - sh:description "Text indicating the availability type of the chemical entity." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:chembl_availability_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:has_attribute ], + sh:order 29 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:chembl_drug_warning ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; - sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:chembl_black_box_warning ] ; + sh:order 27 ; + sh:path dct:description ] ; sh:targetClass biolink:Food . biolink:FoodAdditive a sh:NodeShape ; + rdfs:comment "Any substance which is added to food to preserve or enhance its flavour and/or appearance." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdf:type ], + sh:order 16 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path biolink:chembl_drug_warning ], [ sh:datatype xsd:string ; - sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:chembl_black_box_warning ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:is_toxic ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:equivalent_identifiers ], + sh:order 17 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "Tern indicating the chirality of the chemical entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:chembl_chirality ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a chemical entity is a natural product." ; + sh:order 14 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:chembl_natural_product ], + sh:order 23 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -19001,106 +19097,100 @@ biolink:FoodAdditive a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:chembl_drug_warning ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:provided_by ], + sh:order 26 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; + sh:description "Flag indicating if a chemical entity is a natural product." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:chembl_prodrug ], + sh:order 8 ; + sh:path biolink:chembl_natural_product ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "Text indicating the availability type of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], + sh:order 9 ; + sh:path biolink:chembl_availability_type ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; sh:order 5 ; sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:information_content ], + sh:order 6 ; + sh:path biolink:chembl_prodrug ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:synonym ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "Text indicating the availability type of the chemical entity." ; + sh:description "Tern indicating the chirality of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:chembl_availability_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 10 ; + sh:path biolink:chembl_chirality ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:deprecated ], + sh:order 20 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:chembl_black_box_warning ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:taxon ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ] ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path dct:description ] ; sh:targetClass biolink:FoodAdditive . biolink:FrequencyQualifierMixin a sh:NodeShape ; + rdfs:comment "Qualifier for frequency type associations" ; sh:closed false ; - sh:description "Qualifier for frequency type associations" ; - sh:ignoredProperties ( biolink:has_total biolink:qualified_predicate biolink:has_quotient biolink:subject_aspect_qualifier rdf:type biolink:has_percentage biolink:object_aspect_qualifier biolink:subject_direction_qualifier biolink:sex_qualifier biolink:object_direction_qualifier biolink:disease_context_qualifier biolink:has_count ) ; + sh:ignoredProperties ( biolink:object_direction_qualifier biolink:subject_aspect_qualifier biolink:has_count biolink:has_percentage biolink:has_total biolink:subject_direction_qualifier biolink:object_aspect_qualifier biolink:qualified_predicate rdf:type biolink:disease_context_qualifier biolink:sex_qualifier biolink:has_quotient ) ; sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -19108,13 +19198,6 @@ biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; @@ -19127,169 +19210,135 @@ biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ] ; sh:targetClass biolink:FrequencyQualifierMixin . biolink:FrequencyQuantifier a sh:NodeShape ; + rdfs:comment "A relationship quantifier that expresses how often a relationship holds, using count, total, quotient, or percentage measures." ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_quotient ], + sh:order 3 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_percentage ] ; + sh:path biolink:has_total ] ; sh:targetClass biolink:FrequencyQuantifier . biolink:FunctionalAssociation a sh:NodeShape ; + rdfs:comment "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; sh:closed true ; - sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; sh:ignoredProperties ( rdf:type biolink:species_context_qualifier ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; + sh:property [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 44 ; + sh:path rdf:type ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -19303,127 +19352,125 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_feature_name ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -19437,85 +19484,117 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:order 48 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:FunctionalAssociation . - -biolink:Fungus a sh:NodeShape ; - sh:closed true ; - sh:description "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 46 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ] ; + sh:targetClass biolink:FunctionalAssociation . + +biolink:Fungus a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:information_content ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -19527,12 +19606,16 @@ biolink:Fungus a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:taxon ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -19540,399 +19623,481 @@ biolink:Fungus a sh:NodeShape ; sh:order 1 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ] ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ] ; sh:targetClass biolink:Fungus . biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; + rdfs:comment "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; sh:closed true ; - sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 60 ; - sh:path rdf:type ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "modulation" "allosteric_modulation" "mixed_allosteric_modulation" "biphasic_allosteric_modulation" "mixed_agonism" "positive_modulation" "potentiation" "induction" "cofactor" "activation" "positive_allosteric_modulation" "agonism" "partial_agonism" "biased_agonism" "antibody_agonism" "molecular_channel_opening" "stimulation" "guanyl_nucleotide_exchange" "negative_modulation" "negative_gene_editing_modulation" "gtpase_activation" "atpase_activation" "antisense_oligonucleotide_inhibition" "rna_interference_inhibition" "suppression" "feedback_inhibition" "inhibition" "antibody_inhibition" "antagonism" "allosteric_antagonism" "non_competitive_antagonism" "competitive_inhibition" "noncompetitive_inhibition" "negative_allosteric_modulation" "gating_inhibition" "irreversible_inhibition" "molecular_channel_blockage" "inverse_agonism" "binding" "covalent_binding" "adduction" "crosslinking" "transglutamination" "disuphide_binding" "stabilization" "chaperone_mediated_stabilization" "destabilization" "degradation" "cleavage" "hydrolysis" "disruption" "opening" "multitarget_modulation" "chelation" "release" "sequestration" "oxidoreduction" "exogenous_protein" "exogenous_gene" "transcriptional_regulation" "translational_regulation" "catalytic_activity" "chemical_modification" "relocalization" "isomerization" "signaling_mediated_control" "immune_system_modulation" "vaccine_antigen" "post_transcriptional_regulation" "molecular_modification" "phosphorylation" "dephosphorylation" "neddylation" "deneddylation" "lipidation" "palmitoylation" "myristoylation" "tyrosination" "carboxylation" "ubiquitination" "monoubiquitination" "polyubiquitination" "deubiquitination" "sulfation" "reduction" "oxidation" "acetylation" "deacetylation" "glycosylation" "deglycosylation" "methylation" "trimethylation" "demethylation" "sumoylation" "desumoylation" "ADP-ribosylation" "de-ADP-ribosylation" "ampylation" "hydroxylation" "s_nitrosylation" ) ; + sh:property [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 49 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 63 ; - sh:path biolink:has_attribute ], + sh:order 23 ; + sh:path biolink:sources ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 56 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 31 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path rdf:object ], + sh:order 15 ; + sh:path biolink:species_context_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 51 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:subject_feature_name ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:order 20 ; + sh:path biolink:qualifier ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 16 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:original_subject ], + sh:order 34 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 42 ; sh:path biolink:object_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 59 ; + sh:path biolink:category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 29 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:order 30 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:species_context_qualifier ], + sh:order 41 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 63 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 57 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_label_closure ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 60 ; + sh:path rdf:type ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:qualifiers ], + sh:order 13 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 55 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:has_confidence_score ], [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:object_form_or_variant_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:object_namespace ], + sh:order 43 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 61 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 58 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:subject_namespace ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 27 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_evidence_of_type ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:subject_feature_name ], [ sh:class biolink:AnatomicalEntity ; + sh:description "A qualifier describing the context in which the object of an association holds." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:object_context_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:in ( biolink:causes ) ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 54 ; sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 62 ; sh:path dct:description ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A qualifier describing the context in which the subject of an association holds." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:p_value ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:subject_derivative_qualifier ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" ; + sh:in ( "modulation" "allosteric_modulation" "mixed_allosteric_modulation" "biphasic_allosteric_modulation" "mixed_agonism" "positive_modulation" "potentiation" "induction" "cofactor" "activation" "positive_allosteric_modulation" "agonism" "partial_agonism" "biased_agonism" "antibody_agonism" "molecular_channel_opening" "stimulation" "guanyl_nucleotide_exchange" "negative_modulation" "negative_gene_editing_modulation" "gtpase_activation" "atpase_activation" "antisense_oligonucleotide_inhibition" "rna_interference_inhibition" "suppression" "feedback_inhibition" "inhibition" "antibody_inhibition" "antagonism" "allosteric_antagonism" "non_competitive_antagonism" "competitive_inhibition" "noncompetitive_inhibition" "negative_allosteric_modulation" "gating_inhibition" "irreversible_inhibition" "molecular_channel_blockage" "inverse_agonism" "binding" "covalent_binding" "adduction" "crosslinking" "transglutamination" "disuphide_binding" "stabilization" "chaperone_mediated_stabilization" "destabilization" "degradation" "cleavage" "hydrolysis" "disruption" "opening" "multitarget_modulation" "chelation" "release" "sequestration" "oxidoreduction" "exogenous_protein" "exogenous_gene" "transcriptional_regulation" "translational_regulation" "catalytic_activity" "chemical_modification" "relocalization" "isomerization" "signaling_mediated_control" "immune_system_modulation" "vaccine_antigen" "post_transcriptional_regulation" "molecular_modification" "phosphorylation" "dephosphorylation" "neddylation" "deneddylation" "lipidation" "palmitoylation" "myristoylation" "tyrosination" "carboxylation" "ubiquitination" "monoubiquitination" "polyubiquitination" "deubiquitination" "sulfation" "reduction" "oxidation" "acetylation" "deacetylation" "glycosylation" "deglycosylation" "methylation" "trimethylation" "demethylation" "sumoylation" "desumoylation" "ADP-ribosylation" "de-ADP-ribosylation" "ampylation" "hydroxylation" "s_nitrosylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 12 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:qualifiers ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:qualifier ], + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:timepoint ], + sh:order 32 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 64 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:object_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:original_object ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 61 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:object_derivative_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:knowledge_source ], + sh:order 44 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:affects biolink:ameliorates_condition biolink:disrupts biolink:exacerbates_condition biolink:has_adverse_event biolink:has_side_effect biolink:regulates ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:original_predicate ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 56 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 59 ; - sh:path biolink:category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path rdf:object ] ; + sh:targetClass biolink:GeneAffectsChemicalAssociation . + +biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association in which a gene (e.g., a model-organism ortholog of a known disease gene) serves as a model of a human disease - for example, because mutants of the gene recapitulate core features of the disease." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The relationship to the disease" ; + sh:in ( "biolink:contributes_to" "biolink:associated_with" ), + ( "model_of" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 16 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:object_category ], - [ sh:class biolink:AnatomicalEntity ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:id ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 57 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum). See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:gene2phenotype_confidence_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], + sh:order 38 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; + sh:order 56 ; sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:qualified_predicate ], + sh:order 25 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 8 ; + sh:path biolink:diseases_confidence_score ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 21 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:publications ], + sh:order 42 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 37 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:nodeKind sh:IRI ; + sh:order 58 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 54 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:object_feature_name ] ; - sh:targetClass biolink:GeneAffectsChemicalAssociation . - -biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:publications ], + sh:order 50 ; + sh:path biolink:category ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -19940,283 +20105,214 @@ biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:knowledge_level ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 56 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum). See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:gene2phenotype_confidence_category ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:original_predicate ], + sh:order 41 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path rdf:type ], + sh:order 53 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 55 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 5 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:timepoint ], + sh:order 46 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:sources ], + sh:order 30 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path rdfs:label ], + sh:order 34 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:negated ], + sh:order 36 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:allelic_requirement ; - sh:pattern "^HP:\\d{7}$" ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:object_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 23 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 21 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 44 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 58 ; - sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:subject_feature_name ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:knowledge_source ], - [ sh:description "The relationship to the disease" ; - sh:in ( "biolink:contributes_to" "biolink:associated_with" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 7 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_subject ], + sh:order 59 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 47 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:float ; - sh:description "A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale." ; - sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:diseases_confidence_score ], + sh:order 51 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_namespace ], + sh:order 52 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:category ], + sh:order 19 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 49 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 54 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 33 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:sources ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path dct:description ], + sh:order 43 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:allelic_requirement ; + sh:pattern "^HP:\\d{7}$" ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; @@ -20224,48 +20320,54 @@ biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 22 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:update_date ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 24 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 59 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:retrieval_source_ids ], + sh:order 40 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:id ] ; + sh:order 11 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . biolink:GeneExpressionMixin a sh:NodeShape ; + rdfs:comment "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; sh:closed false ; - sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:LifeStage ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -20277,12 +20379,6 @@ biolink:GeneExpressionMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:phenotypic_state ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], [ sh:class biolink:AnatomicalEntity ; sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; @@ -20292,77 +20388,159 @@ biolink:GeneExpressionMixin a sh:NodeShape ; sh:targetClass biolink:GeneExpressionMixin . biolink:GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation a sh:NodeShape ; + rdfs:comment "Relationship between a gene family and a contained gene or gene product or gene family." ; sh:closed true ; - sh:description "Relationship between a gene family and a contained gene or gene product or gene family." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "membership of a gene or gene product, or strict subset relationship gene family, in the given gene family." ; + sh:in ( biolink:has_active_ingredient biolink:has_excipient biolink:has_food_component biolink:has_nutrient biolink:has_part biolink:has_plasma_membrane_part biolink:has_variant_part ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_subject ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 44 ; + sh:path rdf:type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; @@ -20374,12 +20552,18 @@ biolink:GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -20388,170 +20572,89 @@ biolink:GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation a sh:NodeShape ; sh:order 41 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Gene ; + sh:order 46 ; + sh:path dct:description ], + [ sh:class biolink:GeneFamily ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -20559,27 +20662,21 @@ biolink:GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation a sh:NodeShape ; sh:order 36 ; sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ] ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ] ; sh:targetClass biolink:GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation . biolink:GeneGroupingMixin a sh:NodeShape ; + rdfs:comment "any grouping of multiple genes or gene products" ; sh:closed false ; - sh:description "any grouping of multiple genes or gene products" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; @@ -20589,159 +20686,173 @@ biolink:GeneGroupingMixin a sh:NodeShape ; sh:targetClass biolink:GeneGroupingMixin . biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; + rdfs:comment "A gene-to-disease association that is asserted on the grounds that the gene harbours a sequence variant that contributes to the disease. Qualifies the gene with the form or variant that underlies the contribution." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:category ], + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:publications ], + sh:order 26 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 11 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:supporting_text ], + sh:order 18 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_evidence ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 21 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum). See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:gene2phenotype_confidence_category ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 42 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale." ; + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:diseases_confidence_score ], + sh:order 22 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 44 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 54 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path rdfs:label ], + sh:order 34 ; + sh:path biolink:subject_namespace ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:allelic_requirement ; - sh:pattern "^HP:\\d{7}$" ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:pattern "^HP:\\d{7}$" ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_closure ], + sh:order 50 ; + sh:path biolink:category ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:update_date ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum). See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 6 ; + sh:path biolink:gene2phenotype_confidence_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:subject_category ], + sh:order 38 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; @@ -20749,86 +20860,74 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:order 27 ; sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 7 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 35 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 53 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:object_category_closure ], + sh:order 13 ; + sh:path biolink:publications ], [ sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:in ( "biolink:contributes_to" "biolink:associated_with" ) ; + sh:in ( "biolink:contributes_to" "biolink:associated_with" ), + ( "causes" "contributes_to" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 8 ; sh:path rdf:predicate ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:retrieval_source_ids ], + sh:order 4 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 52 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 55 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:original_predicate ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 31 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:sources ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:semmed_agreement_count ], + sh:order 10 ; + sh:path biolink:negated ], [ sh:class biolink:Disease ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -20836,47 +20935,33 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 54 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:order 33 ; + sh:path biolink:object_category_closure ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_feature_name ], + sh:order 30 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 5 ; + sh:path biolink:diseases_confidence_score ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_confidence_score ], + sh:order 46 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -20884,71 +20969,69 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:order 25 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 51 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:sources ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 49 ; + sh:path biolink:iri ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 7 ; + sh:path rdf:subject ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 47 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ] ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:object_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 21 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:subject_label_closure ] ; sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation a sh:NodeShape ; + rdfs:comment "An association between a gene or gene product or gene family and an anatomical entity." ; sh:closed true ; - sh:description "An association between a gene or gene product or gene family and an anatomical entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:class biolink:GeneOrGeneProductOrGeneFamily ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -20956,80 +21039,34 @@ biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation a sh:NodeShap sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:class biolink:AnatomicalEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -21037,456 +21074,519 @@ biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation a sh:NodeShap sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_feature_name ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_evidence_of_type ] ; - sh:targetClass biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation . - -biolink:GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Relationship between a gene or gene product or gene family to a specified biological process or activity (e.g. molecular activity, biological process or pathway)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 46 ; + sh:path dct:description ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:GeneOrGeneProductOrGeneFamily ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:has_confidence_score ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ] ; + sh:targetClass biolink:GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation . + +biolink:GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation a sh:NodeShape ; + rdfs:comment "Relationship between a gene or gene product or gene family to a specified biological process or activity (e.g. molecular activity, biological process or pathway)." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path dct:description ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:GeneOrGeneProductOrGeneFamily ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:anyURI ; + sh:description "participation of a gene or gene product or gene family in a given biological process or activity (e.g., gene product participates in biological process; gene catalyzes molecular activity; gene family is actively involved in a pathway)." ; + sh:in ( biolink:actively_involved_in biolink:capable_of biolink:catalyzes biolink:consumed_by biolink:enables biolink:is_input_of biolink:is_output_of biolink:is_substrate_of biolink:participates_in ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:BiologicalProcessOrActivity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:anyURI ; - sh:description "participation of a gene or gene product or gene family in a given biological process or activity (e.g., gene product participates in biological process; gene catalyzes molecular activity; gene family is actively involved in a pathway)." ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:BiologicalProcessOrActivity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ] ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ] ; sh:targetClass biolink:GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation . biolink:GeneProductIsoformMixin a sh:NodeShape ; + rdfs:comment "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; sh:closed false ; - sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; @@ -21499,193 +21599,215 @@ biolink:GeneProductIsoformMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:GeneProductIsoformMixin . - -biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Describes a regulatory relationship between two genes or gene products." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; + sh:order 1 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:GeneProductIsoformMixin . + +biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; + rdfs:comment "Describes a regulatory relationship between two genes or gene products." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 49 ; sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:regulates ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 21 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 51 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:qualified_predicate ], + sh:order 27 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:sources ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:evidence_count ], + sh:order 20 ; + sh:path biolink:original_subject ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], + sh:order 31 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 52 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:id ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:elevate_to_prediction ], + sh:order 33 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:sources ], + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], + sh:order 24 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], + sh:order 50 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], + sh:order 41 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:supporting_text ], + sh:order 32 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:in ( biolink:causes ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -21693,695 +21815,482 @@ biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:order 7 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 38 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:iri ], - [ sh:class biolink:GeneOrGeneProduct ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:species_context_qualifier ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 6 ; sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_closure ], + sh:order 44 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:update_date ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:adjusted_p_value ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path rdf:predicate ], + sh:order 36 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], + sh:order 34 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:timepoint ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:object_aspect_qualifier ] ; - sh:targetClass biolink:GeneRegulatesGeneAssociation . - -biolink:GeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( biolink:druggable_gene_category rdf:type biolink:object_aspect_qualifier biolink:subject_direction_qualifier biolink:frequency_qualifier biolink:disease_context_qualifier ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:retrieval_source_ids ], + sh:order 14 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path rdfs:label ], + sh:order 22 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; + sh:order 28 ; sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:qualifier ], + sh:order 30 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:semmed_agreement_count ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 21 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:sources ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 43 ; + sh:path biolink:evidence_count ] ; + sh:targetClass biolink:GeneRegulatesGeneAssociation . + +biolink:GeneToDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association between a gene or gene product and a disease, where variation in the gene is correlated with the disease." ; + sh:closed true ; + sh:ignoredProperties ( biolink:frequency_qualifier biolink:subject_direction_qualifier biolink:object_aspect_qualifier rdf:type biolink:druggable_gene_category biolink:disease_context_qualifier ) ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_supporting_studies ], + sh:order 2 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:subject_category ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:primary_knowledge_source ], + sh:order 32 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:update_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 54 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 30 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_evidence_of_type ], + sh:order 16 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:deprecated ], + sh:order 45 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_feature_name ], + sh:order 34 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; - sh:description "A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:diseases_confidence_score ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:iri ], + sh:order 40 ; + sh:path biolink:adjusted_p_value ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 20 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:negated ], + sh:order 55 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 7 ; - sh:path rdf:subject ], - [ sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:in ( "biolink:contributes_to" "biolink:associated_with" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:object_label_closure ], + sh:order 54 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:allelic_requirement ; - sh:pattern "^HP:\\d{7}$" ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 27 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:original_object ], + sh:order 46 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum). See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:gene2phenotype_confidence_category ], + sh:order 24 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:evidence_count ], + sh:order 47 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_closure ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_confidence_score ], + sh:order 31 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum). See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_namespace ], + sh:order 6 ; + sh:path biolink:gene2phenotype_confidence_category ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:GeneToDiseaseAssociation . - -biolink:GeneToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 48 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:GeneToEntityAssociationMixin . - -biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence_of_type ], + sh:order 28 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 25 ; sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_specialization_qualifier ], + sh:order 52 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category ], + sh:order 50 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 10 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], + sh:order 13 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:object_label_closure ], + sh:order 3 ; + sh:path biolink:allelic_requirement ; + sh:pattern "^HP:\\d{7}$" ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 50 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:update_date ], + sh:order 41 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 51 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 11 ; sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 21 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], + sh:order 26 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; + sh:order 53 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; + [ sh:class biolink:Disease ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], + sh:order 9 ; + sh:path rdf:object ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 14 ; sh:path biolink:sources ], + [ sh:datatype xsd:float ; + sh:description "A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:diseases_confidence_score ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 29 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 7 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_closure ], + sh:order 37 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 39 ; sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( "biolink:contributes_to" "biolink:associated_with" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:elevate_to_prediction ], + sh:minCount 1 ; + sh:order 8 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 49 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:GeneToDiseaseAssociation . + +biolink:GeneToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene that is the subject of the association" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:subject_category_closure ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; - sh:description "expression relationship" ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path rdf:predicate ], + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:GeneToEntityAssociationMixin . + +biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; + rdfs:comment "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_closure ], + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -22394,332 +22303,287 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:LifeStage ; - sh:description "stage at which the gene is expressed in the site" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:stage_qualifier ], + sh:order 50 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:subject_label_closure ], + sh:order 27 ; + sh:path biolink:object_closure ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_feature_name ], + sh:order 43 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:evidence_count ], + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:timepoint ], + sh:order 21 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 51 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "expression relationship" ; + sh:in ( biolink:expressed_in ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:sources ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ] ; - sh:targetClass biolink:GeneToExpressionSiteAssociation . - -biolink:GeneToGeneAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; - sh:ignoredProperties ( biolink:quantifier_qualifier biolink:stage_qualifier biolink:phenotypic_state rdf:type biolink:interacting_molecules_category biolink:expression_site ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 22 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 41 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 42 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 33 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 48 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 25 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 31 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 32 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 36 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:object_specialization_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 20 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 49 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 23 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 11 ; + sh:path biolink:has_evidence_of_type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 44 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 26 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 37 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:LifeStage ; + sh:description "stage at which the gene is expressed in the site" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:stage_qualifier ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; + sh:order 45 ; sh:path biolink:iri ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; + sh:order 3 ; sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:update_date ], + [ sh:class biolink:OntologyClass ; + sh:description "can be used to indicate magnitude, or also ranking" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path rdf:predicate ], + sh:path biolink:quantifier_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:GeneToExpressionSiteAssociation . + +biolink:GeneToGeneAssociation a sh:NodeShape ; + rdfs:comment "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; + sh:closed false ; + sh:ignoredProperties ( biolink:expression_site rdf:type biolink:interacting_molecules_category biolink:stage_qualifier biolink:quantifier_qualifier biolink:phenotypic_state ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -22727,988 +22591,808 @@ biolink:GeneToGeneAssociation a sh:NodeShape ; sh:order 33 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:GeneToGeneAssociation . - -biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:semmed_agreement_count ], + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:supporting_text ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 27 ; + sh:order 23 ; sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; + sh:order 22 ; sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; + sh:order 19 ; sh:path biolink:subject_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; + sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_confidence_score ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; + sh:order 42 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:path biolink:p_value ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 17 ; + sh:order 13 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; - sh:maxCount 1 ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 51 ; + sh:order 47 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; + sh:order 46 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdfs:label ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; - sh:path biolink:stage_qualifier ], + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ] ; - sh:targetClass biolink:GeneToGeneCoexpressionAssociation . + sh:order 8 ; + sh:path biolink:has_evidence_of_type ] ; + sh:targetClass biolink:GeneToGeneAssociation . -biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; +biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; + rdfs:comment "Indicates that two genes are co-expressed, generally under the same conditions." ; sh:closed true ; - sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "membership of the gene in the given gene family." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; + sh:order 28 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; + sh:order 50 ; sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 42 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 4 ; - sh:path biolink:qualifier ], + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 9 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 32 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:order 46 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 39 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; + sh:order 40 ; sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 6 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 51 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 14 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:coexpressed_with ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:sources ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path rdf:type ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:order 17 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 19 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 12 ; sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:GeneToGeneFamilyAssociation . - -biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 10 ; sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_object ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; + sh:order 44 ; sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; + sh:order 49 ; sh:path rdfs:label ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:stage_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 36 ; sh:path biolink:p_value ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 45 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; + sh:order 41 ; sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 21 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "homology relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 24 ; + sh:path biolink:object_feature_name ] ; + sh:targetClass biolink:GeneToGeneCoexpressionAssociation . + +biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; + rdfs:comment "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + [ sh:class biolink:GeneFamily ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ] ; - sh:targetClass biolink:GeneToGeneHomologyAssociation . - -biolink:GeneToGeneProductRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A gene is transcribed and potentially translated to a gene product" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:GeneProductMixin ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "membership of the gene in the given gene family." ; + sh:in ( biolink:member_of ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; @@ -23719,80 +23403,199 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:has_confidence_score ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; - sh:path biolink:id ], + sh:path biolink:id ] ; + sh:targetClass biolink:GeneToGeneFamilyAssociation . + +biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; + rdfs:comment "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "homology relationship type" ; + sh:in ( biolink:homologous_to biolink:orthologous_to biolink:paralogous_to biolink:xenologous_to ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -23800,72 +23603,108 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 42 ; + sh:path biolink:iri ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; @@ -23873,45 +23712,67 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:order 4 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ] ; + sh:targetClass biolink:GeneToGeneHomologyAssociation . + +biolink:GeneToGeneProductRelationship a sh:NodeShape ; + rdfs:comment "A gene is transcribed and potentially translated to a gene product" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -23919,103 +23780,56 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:order 28 ; sh:path biolink:object_namespace ], [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ] ; - sh:targetClass biolink:GeneToGeneProductRelationship . - -biolink:GeneToGoTermAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:has_gene_product ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 44 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -24029,82 +23843,107 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:order 22 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; @@ -24116,51 +23955,93 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:GeneProductMixin ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:GeneToGeneProductRelationship . + +biolink:GeneToGoTermAssociation a sh:NodeShape ; + rdfs:comment "A functional association between a gene (or gene product or macromolecular complex) and a Gene Ontology (GO) term describing the molecular function, biological process, or cellular component in which it participates." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -24168,24 +24049,33 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:order 32 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -24193,93 +24083,134 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:GeneToGoTermAssociation . - -biolink:GeneToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a gene or gene product and a biological process or pathway." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:Gene ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -24287,62 +24218,124 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:GeneToGoTermAssociation . + +biolink:GeneToPathwayAssociation a sh:NodeShape ; + rdfs:comment "An interaction between a gene or gene product and a biological process or pathway." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product entity that participates or influences the pathway" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Pathway ; sh:description "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; @@ -24350,35 +24343,46 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -24391,11 +24395,12 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:has_confidence_score ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -24403,64 +24408,121 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product entity that participates or influences the pathway" ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -24474,82 +24536,84 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:order 19 ; sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:GeneToPathwayAssociation . - -biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_label_closure ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 28 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 60 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:knowledge_level ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 52 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], + sh:order 32 ; + sh:path biolink:p_value ] ; + sh:targetClass biolink:GeneToPathwayAssociation . + +biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "An association between a gene or gene product and a phenotypic feature, where variation in the gene is correlated with the phenotypic feature." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; @@ -24563,226 +24627,194 @@ biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:adjusted_p_value ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_subject ], + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:object_category_closure ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:knowledge_source ], + sh:order 22 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 61 ; sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], + sh:order 41 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 49 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 29 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:has_count ], + sh:order 15 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 40 ; sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:iri ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 48 ; + sh:path biolink:category ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 59 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:allelic_requirement ; - sh:pattern "^HP:\\d{7}$" ], + sh:order 18 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 39 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 62 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:p_value ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_evidence ], + sh:order 26 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 57 ; - sh:path biolink:has_percentage ], + sh:order 56 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_confidence_score ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:allelic_requirement ; + sh:pattern "^HP:\\d{7}$" ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 58 ; sh:path biolink:subject_direction_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 59 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:elevate_to_prediction ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 56 ; - sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:supporting_text ], + sh:order 28 ; + sh:path biolink:subject_closure ], [ sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:in ( "biolink:causes" "biolink:contributes_to" "biolink:associated_with" "biolink:has_phenotype" ) ; sh:maxCount 1 ; @@ -24790,96 +24822,163 @@ biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 5 ; sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:elevate_to_prediction ], + sh:order 8 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 60 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:evidence_count ], + sh:order 54 ; + sh:path biolink:has_count ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 52 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_label_closure ], + sh:order 33 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:original_object ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 57 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 55 ; sh:path biolink:has_total ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 62 ; - sh:path biolink:frequency_qualifier ], + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 50 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:order 36 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_closure ], + sh:order 46 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:update_date ] ; + sh:order 45 ; + sh:path biolink:semmed_agreement_count ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "non_loss_of_function_variant_form" "gain_of_function_variant_form" "dominant_negative_variant_form" "polymorphic_form" "snp_form" "mutant_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . biolink:Genome a sh:NodeShape ; + rdfs:comment "A genome is the sum of genetic material within a cell or virion." ; sh:closed true ; - sh:description "A genome is the sum of genetic material within a cell or virion." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; @@ -24887,209 +24986,214 @@ biolink:Genome a sh:NodeShape ; sh:order 9 ; sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], + sh:order 13 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:taxon ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Genome . biolink:GenomicBackgroundExposure a sh:NodeShape ; + rdfs:comment "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; sh:closed true ; - sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:property [ sh:datatype xsd:integer ; + sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:exposure_start_age ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:exposure_route ], + sh:order 21 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:has_attribute ], + sh:order 27 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:synonym ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:exposure_magnitude ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 11 ; + sh:path biolink:exposure_duration ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:exposure_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path dct:description ], + sh:order 24 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; + [ sh:datatype xsd:string ; + sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path biolink:exposure_additional_condition ], + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:order 10 ; + sh:path biolink:exposure_end_age ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 20 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:exposure_duration ], + sh:order 25 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:exposure_additional_condition ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Type of an exposure event." ; sh:maxCount 1 ; @@ -25102,38 +25206,46 @@ biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:information_content ], - [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; + [ sh:datatype xsd:string ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:exposure_end_age ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:equivalent_identifiers ], + sh:order 22 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Route of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 8 ; + sh:path biolink:exposure_route ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:exposure_type ] ; + sh:order 12 ; + sh:path biolink:exposure_magnitude ] ; sh:targetClass biolink:GenomicBackgroundExposure . biolink:GenomicEntity a sh:NodeShape ; + rdfs:comment "A generically dependent continuant that carries biological sequence that is part of or derived from a genome." ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; @@ -25145,113 +25257,88 @@ biolink:GenomicEntity a sh:NodeShape ; sh:targetClass biolink:GenomicEntity . biolink:GenomicSequenceLocalization a sh:NodeShape ; + rdfs:comment "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:closed true ; - sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:adjusted_p_value ], + sh:property [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:id ], + sh:order 39 ; + sh:path biolink:supporting_text ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 52 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 37 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + sh:order 46 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:start_interbase_coordinate ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_label_closure ], + sh:order 22 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_confidence_score ], - [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; - sh:in ( "+" "-" "." "?" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:genome_build ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], + sh:order 27 ; + sh:path biolink:object_category ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 38 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence_of_type ], + sh:order 10 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 49 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:category ], + sh:order 23 ; + sh:path biolink:original_object ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -25259,90 +25346,98 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:order 19 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:order 25 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:subject_namespace ], + sh:order 41 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:has_sequence_location ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_predicate ], + sh:order 6 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdf:type ], + sh:order 29 ; + sh:path biolink:object_closure ], [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:strand ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:integer ; sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:end_interbase_coordinate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 32 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 7 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:primary_knowledge_source ], + sh:order 44 ; + sh:path biolink:evidence_count ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -25350,127 +25445,150 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:order 18 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 43 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:update_date ], + sh:order 20 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_subject ], + [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + sh:in ( "0" "1" "2" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:phase ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 47 ; sh:path biolink:iri ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:sources ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], + sh:order 36 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path dct:description ], + sh:order 50 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_closure ], + sh:order 24 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 35 ; + sh:path biolink:object_label_closure ], + [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; + sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 2 ; + sh:path biolink:genome_build ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 51 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:elevate_to_prediction ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path rdfs:label ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; + sh:order 15 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ] ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:start_interbase_coordinate ] ; sh:targetClass biolink:GenomicSequenceLocalization . biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association in which a genotype serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:property [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; @@ -25478,74 +25596,135 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 39 ; sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:update_date ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 53 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 54 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 52 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; @@ -25557,87 +25736,68 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 55 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 50 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 49 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 54 ; + sh:path biolink:disease_context_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 52 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -25645,43 +25805,60 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 27 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "The relationship to the disease" ; + sh:in ( biolink:model_of ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:has_confidence_score ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 50 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -25689,44 +25866,45 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 33 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 16 ; + sh:path biolink:original_subject ] ; + sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . + +biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association between a genotype and a disease, in which the genotype (typically a combination of alleles at one or more loci) is linked to the disease state." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -25734,22 +25912,33 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 16 ; sh:path biolink:original_subject ], [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -25757,99 +25946,75 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ] ; - sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . - -biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "E.g. is pathogenic for" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 55 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -25862,67 +26027,37 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:order 47 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 50 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 54 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 52 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -25930,181 +26065,159 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:order 45 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:frequency_qualifier ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:sources ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:order 54 ; + sh:path biolink:disease_context_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 50 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:Disease ; sh:description "a disease that is associated with that genotype" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "E.g. is pathogenic for" ; + sh:in ( biolink:related_condition ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 46 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 52 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:update_date ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ] ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 49 ; + sh:path biolink:subject_aspect_qualifier ] ; sh:targetClass biolink:GenotypeToDiseaseAssociation . biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; @@ -26134,31 +26247,44 @@ biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; sh:targetClass biolink:GenotypeToEntityAssociationMixin . biolink:GenotypeToGeneAssociation a sh:NodeShape ; + rdfs:comment "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; sh:closed true ; - sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -26166,57 +26292,37 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:order 21 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 46 ; + sh:path dct:description ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:anyURI ; - sh:description "the relationship type used to connect genotype to gene" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; @@ -26229,118 +26335,105 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -26348,600 +26441,637 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:anyURI ; + sh:description "the relationship type used to connect genotype to gene" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Gene ; - sh:description "gene implicated in genotype" ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 22 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:Gene ; + sh:description "gene implicated in genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:sources ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ] ; + sh:order 42 ; + sh:path biolink:iri ] ; sh:targetClass biolink:GenotypeToGeneAssociation . biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; + rdfs:comment "Any association between one genotype and a genotypic entity that is a sub-component of it" ; sh:closed true ; - sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Genotype ; + sh:property [ sh:class biolink:Genotype ; sh:description "child genotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:has_variant_part ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:has_confidence_score ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; + sh:order 26 ; + sh:path biolink:object_category_closure ] ; + sh:targetClass biolink:GenotypeToGenotypePartAssociation . + +biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 47 ; + sh:order 48 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path rdfs:label ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:GenotypeToGenotypePartAssociation . - -biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 56 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 58 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 55 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:has_quotient ], + sh:order 47 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path rdf:type ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:has_count ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:has_phenotype ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:IRI ; + sh:order 59 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 52 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 59 ; - sh:path biolink:disease_context_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 57 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sources ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 53 ; sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 21 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:order 40 ; + sh:path biolink:evidence_count ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 60 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; @@ -26949,51 +27079,34 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 5 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 56 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -27001,75 +27114,104 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:id ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 60 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 57 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 51 ; sh:path biolink:has_total ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; + sh:order 54 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 55 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], + sh:order 58 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 20 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ] ; + sh:order 43 ; + sh:path biolink:iri ] ; sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . biolink:GenotypeToVariantAssociation a sh:NodeShape ; + rdfs:comment "Any association between a genotype and a sequence variant." ; sh:closed true ; - sh:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -27077,239 +27219,170 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:order 32 ; sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:anyURI ; - sh:description "the relationship type used to connect genotype to gene" ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_feature_name ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -27317,11 +27390,30 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -27329,87 +27421,111 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ] ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; + rdfs:comment "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; sh:closed true ; - sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -27422,48 +27538,46 @@ biolink:GenotypicSex a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ] ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GenotypicSex . biolink:GeographicExposure a sh:NodeShape ; + rdfs:comment "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; sh:closed true ; - sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:property [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 15 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; sh:maxCount 1 ; @@ -27471,42 +27585,61 @@ biolink:GeographicExposure a sh:NodeShape ; sh:order 7 ; sh:path biolink:exposure_magnitude ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:exposure_type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:exposure_duration ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:exposure_vehicle ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:integer ; + sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], + sh:order 4 ; + sh:path biolink:exposure_start_age ], [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 21 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:deprecated ], + sh:order 19 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -27514,60 +27647,52 @@ biolink:GeographicExposure a sh:NodeShape ; sh:order 16 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; + sh:order 20 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:exposure_type ], + sh:order 23 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:integer ; sh:description "Ending stage of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:exposure_end_age ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:exposure_duration ], [ sh:datatype xsd:string ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdfs:label ], + sh:order 17 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; @@ -27585,69 +27710,29 @@ biolink:GeographicExposure a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ] ; + sh:path biolink:category ] ; sh:targetClass biolink:GeographicExposure . biolink:GeographicLocation a sh:NodeShape ; + rdfs:comment "a location that can be described in lat/long coordinates" ; sh:closed true ; - sh:description "a location that can be described in lat/long coordinates" ; sh:ignoredProperties ( rdf:type biolink:timepoint ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -27655,25 +27740,29 @@ biolink:GeographicLocation a sh:NodeShape ; sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "latitude" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:latitude ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:latitude ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -27681,226 +27770,256 @@ biolink:GeographicLocation a sh:NodeShape ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:float ; sh:description "longitude" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:longitude ] ; - sh:targetClass biolink:GeographicLocation . - -biolink:GeographicLocationAtTime a sh:NodeShape ; - sh:closed true ; - sh:description "a location that can be described in lat/long coordinates, for a particular time" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:path biolink:longitude ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:latitude ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; - sh:description "longitude" ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:longitude ], + sh:order 7 ; + sh:path biolink:information_content ] ; + sh:targetClass biolink:GeographicLocation . + +biolink:GeographicLocationAtTime a sh:NodeShape ; + rdfs:comment "a location that can be described in lat/long coordinates, for a particular time" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ], + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:float ; + sh:description "latitude" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:latitude ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "longitude" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:longitude ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ] ; + sh:path biolink:id ] ; sh:targetClass biolink:GeographicLocationAtTime . biolink:GrossAnatomicalStructure a sh:NodeShape ; + rdfs:comment "An anatomical structure that has more than one cell as a part." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:taxon ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; @@ -27909,31 +28028,42 @@ biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:targetClass biolink:GrossAnatomicalStructure . biolink:Haplotype a sh:NodeShape ; + rdfs:comment "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; sh:closed true ; - sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:information_content ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:taxon ], + sh:order 12 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -27944,11 +28074,18 @@ biolink:Haplotype a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -27956,12 +28093,6 @@ biolink:Haplotype a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -27974,82 +28105,101 @@ biolink:Haplotype a sh:NodeShape ; sh:order 15 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:Haplotype . + +biolink:Hospitalization a sh:NodeShape ; + rdfs:comment "The admission and care of a patient in a hospital for observation, diagnosis, or treatment." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 9 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Haplotype . - -biolink:Hospitalization a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -28062,57 +28212,28 @@ biolink:Hospitalization a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:information_content ] ; sh:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; + rdfs:comment "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization." ; sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:HospitalizationOutcome . biolink:Human a sh:NodeShape ; sh:closed true ; - sh:description "A member of the the species Homo sapiens." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; @@ -28121,133 +28242,143 @@ biolink:Human a sh:NodeShape ; sh:order 1 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ] ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Human . biolink:IceesStudyResult a sh:NodeShape ; + rdfs:comment "A study result that represents a result, from a supporting Study, which is specifically associated with an Integrated Clinical and Environmental Exposures Service (ICEES) knowledge assertion." ; sh:closed true ; - sh:description "A study result that represents a result, from a supporting Study, which is specifically associated with an Integrated Clinical and Environmental Exposures Service (ICEES) knowledge assertion." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:integer ; + sh:description "Degrees of freedom (dof) in a chi-squared test referring to the number of values in the final calculation of a statistic that are free to vary" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:chi_squared_dof ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:full_name ], + sh:order 19 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; - sh:description "The chi-square p-value tells you the probability that the observed differences (or associations) in your data occurred by random chance, assuming the null hypothesis is true." ; + sh:description "The natural logarithm of the odds ratio (OR), or the ratio of the odds of an event Y occurring in an exposed group versus the odds of an event Y occurring in a non-exposed group." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:chi_squared_p ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 6 ; + sh:path biolink:log_odds_ratio ], + [ sh:datatype xsd:float ; + sh:description "The chi-squared statistic measures how much observed data deviate from expected values under the null hypothesis." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path biolink:chi_squared_statistic ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -28255,15 +28386,27 @@ biolink:IceesStudyResult a sh:NodeShape ; sh:order 20 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The natural logarithm of the odds ratio (OR), or the ratio of the odds of an event Y occurring in an exposed group versus the odds of an event Y occurring in a non-exposed group." ; + sh:order 11 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:integer ; + sh:description "The total number of patients or participants within a sample population." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:log_odds_ratio ], + sh:order 3 ; + sh:path biolink:total_sample_size ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -28271,225 +28414,149 @@ biolink:IceesStudyResult a sh:NodeShape ; sh:order 17 ; sh:path biolink:category ], [ sh:datatype xsd:float ; - sh:description """The Fisher Exact Test is used to determine whether there is a non-random association between two categorical variables in a 2×2 contingency table, especially when sample sizes are small. The odds ratio (OR) quantifies the strength of that association. - OR = 1 implies No association - OR > 1 implies Positive association (Group A more likely to have Outcome 1) - OR < 1 implies Negative association (Group A less likely to have Outcome 1)""" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:fisher_exact_odds_ratio ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The chi-squared statistic measures how much observed data deviate from expected values under the null hypothesis." ; - sh:maxCount 1 ; + sh:description "The ninety-five percent confidence range in which the true log odds ratio for the sample population falls. To calculate the 95% confidence interval (CI) for a log odds ratio (a pair of numbers), you need the standard error (SE) of the log odds ratio. This interval helps you understand the precision of your estimate and whether the association is statistically significant." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:chi_squared_statistic ], + sh:order 7 ; + sh:path biolink:log_odds_ratio_95_ci ], [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The chi-square p-value tells you the probability that the observed differences (or associations) in your data occurred by random chance, assuming the null hypothesis is true." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "The total number of patients or participants within a sample population." ; + sh:order 2 ; + sh:path biolink:chi_squared_p ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:total_sample_size ], + sh:order 10 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "The Fisher exact p-value tells you the probability of observing a table as extreme as (or more extreme than) your actual data, assuming that the null hypothesis of independence is true. It's most commonly used for 2×2 contingency tables, especially when sample sizes are small or expected counts are low." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:fisher_exact_p ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 16 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:datatype xsd:float ; + sh:description """The Fisher Exact Test is used to determine whether there is a non-random association between two categorical variables in a 2×2 contingency table, especially when sample sizes are small. The odds ratio (OR) quantifies the strength of that association. + OR = 1 implies No association + OR > 1 implies Positive association (Group A more likely to have Outcome 1) + OR < 1 implies Negative association (Group A less likely to have Outcome 1)""" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:integer ; - sh:description "Degrees of freedom (dof) in a chi-squared test referring to the number of values in the final calculation of a statistic that are free to vary" ; + sh:order 4 ; + sh:path biolink:fisher_exact_odds_ratio ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:chi_squared_dof ], + sh:order 14 ; + sh:path biolink:taxon ], [ sh:datatype xsd:float ; - sh:description "The ninety-five percent confidence range in which the true log odds ratio for the sample population falls. To calculate the 95% confidence interval (CI) for a log odds ratio (a pair of numbers), you need the standard error (SE) of the log odds ratio. This interval helps you understand the precision of your estimate and whether the association is statistically significant." ; + sh:description "The Fisher exact p-value tells you the probability of observing a table as extreme as (or more extreme than) your actual data, assuming that the null hypothesis of independence is true. It's most commonly used for 2×2 contingency tables, especially when sample sizes are small or expected counts are low." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:log_odds_ratio_95_ci ] ; + sh:order 5 ; + sh:path biolink:fisher_exact_p ] ; sh:targetClass biolink:IceesStudyResult . biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; + rdfs:comment "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:closed true ; - sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -28501,41 +28568,45 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -28543,85 +28614,134 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:mentions ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:update_date ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; @@ -28629,166 +28749,164 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:order 39 ; sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ] ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ] ; sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . biolink:Invertebrate a sh:NodeShape ; sh:closed true ; - sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Invertebrate . biolink:JournalArticle a sh:NodeShape ; + rdfs:comment "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:closed true ; - sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], + sh:order 11 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:volume ], - [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:issue ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:order 28 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:equivalent_identifiers ], + sh:order 14 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:format ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], + [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:issue ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], + sh:order 24 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; @@ -28796,23 +28914,49 @@ biolink:JournalArticle a sh:NodeShape ; sh:order 25 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 26 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:taxon ], + sh:order 16 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:pages ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:rights ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -28820,63 +28964,62 @@ biolink:JournalArticle a sh:NodeShape ; sh:order 23 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:pages ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 17 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:information_content ], + sh:order 20 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:license ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 21 ; + sh:path biolink:id ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:creation_date ], + sh:order 19 ; + sh:path biolink:information_content ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:rights ], + sh:order 6 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:keywords ], + sh:order 15 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:mesh_terms ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -28884,33 +29027,18 @@ biolink:JournalArticle a sh:NodeShape ; sh:order 22 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path rdf:type ] ; + sh:order 13 ; + sh:path biolink:format ] ; sh:targetClass biolink:JournalArticle . biolink:KnowledgeGraph a sh:NodeShape ; + rdfs:comment "A container representing a knowledge graph serialized in KGX (Knowledge Graph Exchange) format. A KnowledgeGraph aggregates a collection of nodes (entities) and edges (relationships between entities) conforming to the KGX specification, enabling interoperable exchange of biomedical knowledge graphs across tools and systems in the Biolink ecosystem.", + "A knowledge graph is a structured representation of knowledge in the form of a graph, where nodes represent entities or concepts, and edges represent relationships between them. Knowledge graphs are used to organize and connect information from various sources, enabling better understanding, analysis, and reasoning about complex domains." ; sh:closed false, true ; - sh:description "A knowledge graph is a structured representation of knowledge in the form of a graph, where nodes represent entities or concepts, and edges represent relationships between them. Knowledge graphs are used to organize and connect information from various sources, enabling better understanding, analysis, and reasoning about complex domains.", - "A knowledge graph represented in KGX format" ; sh:ignoredProperties ( rdf:type ), ( rdf:type ) ; sh:property [ sh:class biolink:Association ; @@ -28936,8 +29064,8 @@ biolink:KnowledgeGraph a sh:NodeShape ; sh:targetClass biolink:KnowledgeGraph . biolink:LogOddsAnalysisResult a sh:NodeShape ; + rdfs:comment "A result of a log odds ratio analysis." ; sh:closed true ; - sh:description "A result of a log odds ratio analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; @@ -28945,60 +29073,61 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 6 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -29006,53 +29135,62 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ] ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ] ; sh:targetClass biolink:LogOddsAnalysisResult . biolink:MacromolecularComplex a sh:NodeShape ; + rdfs:comment "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:closed true ; - sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:information_content ], + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -29064,198 +29202,178 @@ biolink:MacromolecularComplex a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; + sh:order 8 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ] ; - sh:targetClass biolink:MacromolecularComplex . - -biolink:MacromolecularMachineHasSubstrateAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Describes the relationship between an enzyme (usually a macromolecular complex or gene product) and the molecules it acts on (substrate). The substrate can be a chemical, a polypeptide, or a protein." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 9 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 10 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 16 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:MacromolecularComplex . + +biolink:MacromolecularMachineHasSubstrateAssociation a sh:NodeShape ; + rdfs:comment "Describes the relationship between an enzyme (usually a macromolecular complex or gene product) and the molecules it acts on (substrate). The substrate can be a chemical, a polypeptide, or a protein." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:ChemicalEntityOrProteinOrPolypeptide ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -29263,123 +29381,94 @@ biolink:MacromolecularMachineHasSubstrateAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:ChemicalEntityOrProteinOrPolypeptide ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -29388,378 +29477,485 @@ biolink:MacromolecularMachineHasSubstrateAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:has_substrate ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; - sh:path biolink:has_confidence_score ] ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:MacromolecularMachineHasSubstrateAssociation . biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; + rdfs:comment "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:category ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], + sh:order 44 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], + sh:order 47 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:supporting_text ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], + sh:order 43 ; + sh:path biolink:iri ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:sources ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:BiologicalProcess ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], + sh:order 42 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], + sh:order 46 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdf:type ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:BiologicalProcess ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:class biolink:OrganismTaxon ; sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 49 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ] ; + sh:order 48 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; + rdfs:comment "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 20 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:CellularComponent ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 48 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], + sh:order 37 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 21 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -29767,12 +29963,28 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; @@ -29784,223 +29996,149 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:order 42 ; + sh:path biolink:id ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], + sh:order 8 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], + sh:order 46 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:CellularComponent ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 36 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ] ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; + rdfs:comment "an association which has a macromolecular machine mixin as a subject" ; sh:closed false ; - sh:description "an association which has a macromolecular machine mixin as a subject" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -30019,78 +30157,87 @@ biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; + rdfs:comment "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:order 38 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 49 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 48 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -30102,329 +30249,313 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 37 ; + sh:path biolink:update_date ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sources ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], - [ sh:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:order 46 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:order 40 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 47 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], + sh:order 42 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], + sh:order 21 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 20 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ], + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:species_context_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ] ; + sh:order 23 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . biolink:Mammal a sh:NodeShape ; sh:closed true ; - sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ] ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Mammal . biolink:MappingCollection a sh:NodeShape ; + rdfs:comment "An abstract container class that holds a set of predicate mappings. Serves as a top-level root for documents that enumerate how third-party or deprecated predicates should be rewritten to Biolink predicates and their associated qualifiers." ; sh:closed false ; - sh:description "A collection of deprecated mappings." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:PredicateMapping ; sh:description "A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3." ; @@ -30434,32 +30565,37 @@ biolink:MappingCollection a sh:NodeShape ; sh:targetClass biolink:MappingCollection . biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; + rdfs:comment "An association between a material sample and the material entity from which it is derived." ; sh:closed true ; - sh:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30467,67 +30603,119 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:NamedThing ; sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; sh:maxCount 1 ; @@ -30535,34 +30723,24 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; @@ -30570,85 +30748,63 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:order 37 ; sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:anyURI ; sh:description "derivation relationship" ; + sh:in ( biolink:derives_from biolink:is_metabolite_of ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -30656,383 +30812,366 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:order 36 ; sh:path biolink:update_date ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ] ; + sh:targetClass biolink:MaterialSampleDerivationAssociation . + +biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "An association between a material sample and a disease or phenotype." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 21 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 48 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 32 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ] ; - sh:targetClass biolink:MaterialSampleDerivationAssociation . - -biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a material sample and a disease or phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 50 ; + sh:path dct:description ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:update_date ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], + sh:order 52 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:iri ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:sources ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:disease_context_qualifier ], + sh:order 13 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:id ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:evidence_count ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 17 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:update_date ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_closure ], + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:timepoint ], + sh:order 20 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_specialization_qualifier ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 42 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 49 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 3 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence_of_type ], + sh:order 51 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:subject_specialization_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 34 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], + sh:order 46 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_confidence_score ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 37 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:deprecated ], + sh:order 19 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], + sh:order 6 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 22 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:subject_namespace ] ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_confidence_score ] ; sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; + rdfs:comment "An association between a material sample and something." ; sh:closed false ; - sh:description "An association between a material sample and something." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:MaterialSample ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -31045,47 +31184,39 @@ biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:predicate ] ; sh:targetClass biolink:MaterialSampleToEntityAssociationMixin . biolink:MicroRNA a sh:NodeShape ; + rdfs:comment "A small (~22 nucleotide) RNA molecule that is the endogenous transcript of a miRNA gene. Produced from precursor molecules that form hairpin structures, which are processed (typically via the Dicer pathway) to yield a single miRNA molecule. miRNAs function by triggering cleavage of target molecules or acting as translational repressors." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -31093,20 +31224,23 @@ biolink:MicroRNA a sh:NodeShape ; sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -31120,44 +31254,44 @@ biolink:MicroRNA a sh:NodeShape ; sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ] ; + sh:order 10 ; + sh:path biolink:iri ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; + rdfs:comment "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" ; sh:closed false ; - sh:description "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; @@ -31166,265 +31300,122 @@ biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:ModelToDiseaseAssociationMixin . - -biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:description "The relationship to the disease" ; + sh:in ( biolink:model_of ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:ModelToDiseaseAssociationMixin . + +biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; + rdfs:comment "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:sources ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 43 ; + sh:path biolink:category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -31432,94 +31423,90 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . - -biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -31527,113 +31514,215 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:order 46 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . + +biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; + rdfs:comment "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; @@ -31646,39 +31735,39 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -31686,16 +31775,34 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -31703,259 +31810,291 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:order 27 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path rdfs:label ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; + rdfs:comment "Association that holds the relationship between a reaction and the pathway it participates in." ; sh:closed true ; - sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:food_component_of biolink:is_active_ingredient_of biolink:is_excipient_of biolink:nutrient_of biolink:part_of biolink:plasma_membrane_part_of biolink:variant_part_of ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -31963,44 +32102,50 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -32008,101 +32153,74 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Pathway ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ] ; + sh:order 3 ; + sh:path biolink:negated ] ; sh:targetClass biolink:MolecularActivityToPathwayAssociation . biolink:MolecularMixture a sh:NodeShape ; + rdfs:comment "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; sh:closed true ; - sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; + sh:description "Tern indicating the chirality of the chemical entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 14 ; + sh:path biolink:chembl_chirality ], + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a chemical entity is a natural product." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:chembl_natural_product ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:taxon ], + sh:order 17 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Text indicating the availability type of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:chembl_availability_type ], + [ sh:datatype xsd:string ; + sh:description "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:chembl_drug_warning ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -32110,83 +32228,82 @@ biolink:MolecularMixture a sh:NodeShape ; sh:order 29 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:provided_by ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 23 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:xref ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 10 ; + sh:path biolink:chembl_prodrug ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:information_content ], + sh:order 22 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:chembl_prodrug ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:chembl_black_box_warning ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; - sh:order 9 ; - sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:has_attribute ], + sh:order 15 ; + sh:path biolink:chembl_drug_warning ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; - sh:description "Tern indicating the chirality of the chemical entity." ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:chembl_chirality ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -32194,219 +32311,178 @@ biolink:MolecularMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a chemical entity is a natural product." ; + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; + sh:order 9 ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:chembl_natural_product ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:order 21 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ] ; + sh:order 27 ; + sh:path dct:description ] ; sh:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; + rdfs:comment "An outcome of death from resulting from an exposure event." ; sh:closed true ; - sh:description "An outcome of death from resulting from an exposure event." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:MortalityOutcome . biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape ; + rdfs:comment "An association in which the subject entity is linked to the likelihood of the object entity occurring, manifesting, or being observed. Subject and object may each be qualified by aspect and context, and the association may be further qualified by a population context." ; sh:closed true ; - sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 52 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_label_closure ], + sh:order 29 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; + sh:description "A qualifier describing the context in which the object of an association holds." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:order 40 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:population_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:deprecated ], + sh:order 43 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path dct:description ], + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:object_namespace ], + sh:order 23 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_feature_name ], + sh:order 20 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_closure ], + sh:order 39 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:knowledge_source ], + sh:order 25 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 51 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 37 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:order 41 ; + sh:path biolink:update_date ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 28 ; + sh:path biolink:subject_closure ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -32414,51 +32490,107 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:nodeKind sh:IRI ; sh:order 4 ; sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "A qualifier describing the context in which the subject of an association holds." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:subject_context_qualifier ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 18 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 34 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 52 ; + sh:path biolink:has_attribute ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:elevate_to_prediction ], + sh:order 47 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 24 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:population_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 33 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_confidence_score ], + sh:order 46 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -32472,59 +32604,65 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:evidence_count ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_label_closure ], + sh:order 42 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:semmed_agreement_count ], + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:associated_with biolink:associated_with_decreased_likelihood_of biolink:associated_with_increased_likelihood_of biolink:associated_with_likelihood_of biolink:associated_with_resistance_to biolink:associated_with_response_to biolink:associated_with_sensitivity_to biolink:biomarker_for biolink:coexpressed_with biolink:condition_associated_with_gene biolink:correlated_with biolink:decreased_likelihood_associated_with biolink:gene_associated_with_condition biolink:genetic_association biolink:genetically_associated_with biolink:has_biomarker biolink:increased_likelihood_associated_with biolink:likelihood_associated_with biolink:negatively_correlated_with biolink:occurs_together_in_literature_with biolink:positively_correlated_with biolink:resistance_associated_with biolink:response_associated_with biolink:sensitivity_associated_with ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_feature_name ], + sh:order 45 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:negated ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:sources ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category ], + sh:order 5 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:deprecated ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -32534,64 +32672,61 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . biolink:Node a sh:NodeShape ; + rdfs:comment "A generic node in a KGX-formatted knowledge graph, representing a single entity or concept with a unique identifier. This class serves as the structural superclass for `named thing` in Biolink, providing the minimal KGX-compliant contract (identifier, category, etc.) that any biolink entity participating in a knowledge graph must satisfy." ; sh:closed true ; - sh:description "A node in a KGX graph, will be superclass for named thing" ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:Node . biolink:NoncodingRNAProduct a sh:NodeShape ; + rdfs:comment "An RNA transcript that does not encode for a protein rather the RNA molecule is the functional gene product." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -32599,6 +32734,21 @@ biolink:NoncodingRNAProduct a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -32611,173 +32761,153 @@ biolink:NoncodingRNAProduct a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; + sh:order 4 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:NoncodingRNAProduct . biolink:NucleicAcidSequenceMotif a sh:NodeShape ; + rdfs:comment "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. consensus sequences." ; sh:closed true ; - sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:information_content ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ] ; + sh:path biolink:information_content ] ; sh:targetClass biolink:NucleicAcidSequenceMotif . biolink:NucleosomeModification a sh:NodeShape ; + rdfs:comment "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform." ; sh:closed true ; - sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:information_content ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -32785,26 +32915,16 @@ biolink:NucleosomeModification a sh:NodeShape ; sh:order 12 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; @@ -32812,11 +32932,18 @@ biolink:NucleosomeModification a sh:NodeShape ; sh:order 0 ; sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -32824,50 +32951,72 @@ biolink:NucleosomeModification a sh:NodeShape ; sh:order 15 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:order 8 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ] ; + sh:order 16 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:NucleosomeModification . biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; + rdfs:comment "A result of a observed expected frequency analysis." ; sh:closed true ; - sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -32875,35 +33024,16 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:order 8 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -32911,41 +33041,54 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:order 6 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:equivalent_identifiers ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:Occurrent a sh:NodeShape ; + rdfs:comment "A processual entity." ; sh:closed false ; - sh:description "A processual entity." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:Occurrent . biolink:OrganismAttribute a sh:NodeShape ; + rdfs:comment "describes a characteristic of an organismal entity." ; sh:closed true ; - sh:description "describes a characteristic of an organismal entity." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; @@ -32953,52 +33096,18 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -33011,64 +33120,99 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdf:type ] ; sh:targetClass biolink:OrganismAttribute . biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; + rdfs:comment "An association between an organism taxon and another entity" ; sh:closed false ; - sh:description "An association between an organism taxon and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OrganismTaxon ; sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -33079,76 +33223,48 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; sh:targetClass biolink:OrganismTaxonToEntityAssociation . biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; + rdfs:comment "An abstract association between an organism taxon and an environmental context (e.g., a habitat, biome, or ecological setting) in which the taxon occurs." ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -33157,84 +33273,115 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:NamedThing ; - sh:description "the environment in which the organism occurs" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -33242,277 +33389,224 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:order 21 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "predicate describing the relationship between the taxon and the environment" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . - -biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "A relationship between two organism taxon nodes" ; - sh:ignoredProperties ( rdf:type biolink:associated_environmental_context ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:datatype xsd:anyURI ; + sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "the environment in which the organism occurs" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:class biolink:RetrievalSource ; + sh:order 15 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . + +biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; + rdfs:comment "A relationship between two organism taxon nodes" ; + sh:closed false ; + sh:ignoredProperties ( rdf:type biolink:associated_environmental_context ) ; + sh:property [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:sources ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -33521,274 +33615,270 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_feature_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . - -biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . + +biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; + rdfs:comment "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 49 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], + sh:order 42 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], + sh:order 21 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], + sh:order 35 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 45 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -33796,61 +33886,74 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:order 23 ; sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:associated_environmental_context ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 48 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "the environment in which the two taxa interact" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:associated_environmental_context ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 36 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; @@ -33858,224 +33961,302 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:order 40 ; sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], + sh:order 43 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:knowledge_level ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:has_confidence_score ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 46 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . - -biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; - sh:closed true ; - sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 37 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:binds biolink:directly_physically_interacts_with biolink:gene_fusion_with biolink:genetic_neighborhood_of biolink:genetically_interacts_with biolink:indirectly_physically_interacts_with biolink:interacts_with biolink:pharmacologically_interacts_with biolink:physically_interacts_with biolink:regulates ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:order 18 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OrganismTaxon ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path dct:description ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . + +biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; + rdfs:comment "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "the more specific taxon" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:subclass_of ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34083,228 +34264,335 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more general taxon" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:deprecated ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; + sh:order 42 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . + +biolink:OrganismToOrganismAssociation a sh:NodeShape ; + rdfs:comment "An association between two individual organisms (e.g., symbiosis, parasitism, predation, or other inter-organism relationships)." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:IndividualOrganism ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . - -biolink:OrganismToOrganismAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:update_date ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -34316,47 +34604,35 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:class biolink:IndividualOrganism ; sh:description "An association between two individual organisms." ; sh:maxCount 1 ; @@ -34365,157 +34641,194 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 14 ; + sh:path biolink:agent_type ] ; + sh:targetClass biolink:OrganismToOrganismAssociation . + +biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association in which an organismal entity (e.g., a strain or breed) serves as a model of a disease, either because it has a natural predisposition to the disease or was bred or engineered specifically to recapitulate it." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:sources ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 53 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OrganismalEntity ; + sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 49 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_feature_name ], - [ sh:class biolink:IndividualOrganism ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 52 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 50 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 55 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:OrganismToOrganismAssociation . - -biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -34527,605 +34840,441 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:class biolink:OrganismalEntity ; - sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 43 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 50 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 54 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "The relationship to the disease" ; + sh:in ( biolink:model_of ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:qualified_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 52 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 54 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ] ; + sh:order 10 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; + rdfs:comment "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; sh:closed true ; - sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; - sh:ignoredProperties ( biolink:interacting_molecules_category rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:ignoredProperties ( rdf:type biolink:interacting_molecules_category ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:class biolink:EvidenceType ; sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "interaction relationship type" ; + sh:in ( biolink:binds biolink:directly_physically_interacts_with biolink:gene_fusion_with biolink:genetic_neighborhood_of biolink:genetically_interacts_with biolink:indirectly_physically_interacts_with biolink:interacts_with biolink:pharmacologically_interacts_with biolink:physically_interacts_with biolink:regulates ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "interaction relationship type" ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:PairwiseGeneToGeneInteraction . biolink:PairwiseMolecularInteraction a sh:NodeShape ; + rdfs:comment "An interaction at the molecular level between two physical entities" ; sh:closed true ; - sh:description "An interaction at the molecular level between two physical entities" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; @@ -35133,6 +35282,11 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:evidence_count ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; sh:maxCount 1 ; @@ -35140,35 +35294,18 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:order 43 ; + sh:path biolink:iri ], [ sh:class biolink:MolecularEntity ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -35176,160 +35313,205 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "interaction relationship type" ; + sh:in ( biolink:binds biolink:directly_physically_interacts_with biolink:gene_fusion_with biolink:genetic_neighborhood_of biolink:genetically_interacts_with biolink:indirectly_physically_interacts_with biolink:interacts_with biolink:pharmacologically_interacts_with biolink:physically_interacts_with biolink:regulates ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], + sh:order 49 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:supporting_text ], + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 48 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:anyURI ; - sh:description "interaction relationship type" ; + sh:order 21 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 46 ; + sh:path rdfs:label ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:sources ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:OntologyClass ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:MolecularEntity ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 47 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 37 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], + sh:order 38 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; @@ -35341,126 +35523,61 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:object_namespace ], - [ sh:class biolink:MolecularEntity ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 20 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 45 ; + sh:path rdf:type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ] ; + sh:order 11 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:PairwiseMolecularInteraction . biolink:Patent a sh:NodeShape ; + rdfs:comment "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; sh:closed true ; - sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], + sh:order 23 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:keywords ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; @@ -35468,11 +35585,40 @@ biolink:Patent a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:pages ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -35480,25 +35626,15 @@ biolink:Patent a sh:NodeShape ; sh:order 12 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:mesh_terms ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; @@ -35509,88 +35645,99 @@ biolink:Patent a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:summary ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 15 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:format ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ] ; + sh:order 18 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Patent . biolink:PathognomonicityQuantifier a sh:NodeShape ; + rdfs:comment "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease" ; sh:closed false ; - sh:description "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease" ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:PathognomonicityQuantifier . biolink:PathologicalAnatomicalExposure a sh:NodeShape ; + rdfs:comment "An abnormal anatomical structure, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome." ; sh:closed true ; - sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:exposure_magnitude ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:iri ], + sh:order 18 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Type of an exposure event." ; + sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:exposure_vehicle ], + sh:order 8 ; + sh:path biolink:exposure_additional_condition ], [ sh:datatype xsd:integer ; sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; @@ -35598,40 +35745,23 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:order 4 ; sh:path biolink:exposure_start_age ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:exposure_route ], - [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_end_age ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:category ], + sh:order 17 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:exposure_type ], [ sh:datatype xsd:string ; sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; sh:maxCount 1 ; @@ -35640,11 +35770,21 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:order 9 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -35652,136 +35792,137 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:order 21 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 1 ; + sh:path biolink:exposure_type ], + [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:exposure_duration ], [ sh:datatype xsd:string ; + sh:description "Type of an exposure event." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path biolink:exposure_vehicle ], [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:exposure_additional_condition ], + sh:order 20 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path biolink:exposure_magnitude ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:taxon ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:exposure_duration ], + sh:order 5 ; + sh:path biolink:exposure_end_age ], + [ sh:datatype xsd:string ; + sh:description "Route of exposure." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:exposure_route ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ] ; + sh:path biolink:equivalent_identifiers ] ; sh:targetClass biolink:PathologicalAnatomicalExposure . biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; + rdfs:comment "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." ; sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:PathologicalAnatomicalOutcome . biolink:PathologicalAnatomicalStructure a sh:NodeShape ; + rdfs:comment "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:closed true ; - sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:information_content ], + sh:order 9 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -35789,192 +35930,184 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:order 13 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 7 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ] ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:PathologicalAnatomicalStructure . biolink:PathologicalEntityMixin a sh:NodeShape ; + rdfs:comment "A pathological (abnormal) structure or process." ; sh:closed false ; - sh:description "A pathological (abnormal) structure or process." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:PathologicalEntityMixin . biolink:PathologicalProcess a sh:NodeShape ; + rdfs:comment "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:closed true ; - sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], + sh:order 19 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], + sh:order 16 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:category ] ; sh:targetClass biolink:PathologicalProcess . biolink:PathologicalProcessExposure a sh:NodeShape ; + rdfs:comment "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome." ; sh:closed true ; - sh:description "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_end_age ], - [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:exposure_route ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:integer ; + sh:property [ sh:datatype xsd:integer ; sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:exposure_start_age ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; sh:maxCount 1 ; @@ -35982,120 +36115,144 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:order 7 ; sh:path biolink:exposure_magnitude ], [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 21 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "Additional conditions impacting an exposure event." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:exposure_additional_condition ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:exposure_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Type of exposure" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:exposure_type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:full_name ], + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:exposure_end_age ], + [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:exposure_duration ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:exposure_additional_condition ], + sh:order 23 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; + sh:order 2 ; + sh:path biolink:exposure_vehicle ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:exposure_duration ], + sh:order 15 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Type of an exposure event." ; + sh:description "Route of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:exposure_vehicle ] ; + sh:order 3 ; + sh:path biolink:exposure_route ], + [ sh:datatype xsd:string ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path rdf:type ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; + rdfs:comment "An outcome resulting from an exposure event which is the manifestation of a pathological process." ; sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of a pathological process." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:PathologicalProcessOutcome . biolink:Phenomenon a sh:NodeShape ; + rdfs:comment "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; sh:closed true ; - sh:description "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -36103,43 +36260,43 @@ biolink:Phenomenon a sh:NodeShape ; sh:order 9 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -36148,75 +36305,85 @@ biolink:Phenomenon a sh:NodeShape ; sh:order 7 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ] ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Phenomenon . biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association between a phenotypic feature (sign or symptom) and a disease, where the phenotypic feature is a manifestation or clinical indicator of the disease." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 55 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path rdfs:label ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:sources ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 59 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -36224,68 +36391,69 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:double ; + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 43 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:has_count ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 53 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 49 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 48 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 52 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 37 ; + sh:path biolink:update_date ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -36293,68 +36461,62 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:order 34 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 59 ; - sh:path biolink:frequency_qualifier ], + sh:order 38 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 60 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:has_total ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], + sh:order 54 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; @@ -36362,183 +36524,204 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:order 58 ; sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], + sh:order 35 ; + sh:path biolink:supporting_text ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:agent_type ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 60 ; - sh:path biolink:disease_context_qualifier ], + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 57 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:associated_with biolink:associated_with_decreased_likelihood_of biolink:associated_with_increased_likelihood_of biolink:associated_with_likelihood_of biolink:associated_with_resistance_to biolink:associated_with_response_to biolink:associated_with_sensitivity_to biolink:biomarker_for biolink:coexpressed_with biolink:condition_associated_with_gene biolink:correlated_with biolink:decreased_likelihood_associated_with biolink:gene_associated_with_condition biolink:genetic_association biolink:genetically_associated_with biolink:has_biomarker biolink:increased_likelihood_associated_with biolink:likelihood_associated_with biolink:negatively_correlated_with biolink:occurs_together_in_literature_with biolink:positively_correlated_with biolink:resistance_associated_with biolink:response_associated_with biolink:sensitivity_associated_with ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 56 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 57 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 45 ; + sh:path rdf:type ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 50 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], + sh:order 51 ; + sh:path biolink:has_total ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ] ; + sh:order 42 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ] ; sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; + rdfs:comment "A mixin applied to any association whose subject (source node) is a phenotypic feature." ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_percentage ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -36546,305 +36729,309 @@ biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path rdf:subject ], + sh:order 13 ; + sh:path rdf:object ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 11 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:has_total ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualified_predicate ], + sh:order 5 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_quotient ] ; + sh:path biolink:sex_qualifier ] ; sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; sh:closed true ; - sh:description "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 20 ; + sh:path biolink:subject_feature_name ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 55 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:has_total ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 59 ; sh:path biolink:disease_context_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 48 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:category ], + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_feature_name ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 60 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 56 ; sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path rdf:type ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:has_percentage ], + sh:order 37 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:supporting_text ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 58 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 55 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], + sh:order 46 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sources ], [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], + sh:order 50 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 3 ; + sh:path rdf:object ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], + sh:order 49 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:has_count ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 58 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -36852,154 +37039,113 @@ biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 34 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:double ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 43 ; + sh:path biolink:iri ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 40 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 60 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 53 ; + sh:path biolink:has_percentage ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 57 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 54 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 51 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ] ; + sh:order 52 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . biolink:PhenotypicQuality a sh:NodeShape ; + rdfs:comment "A characteristic of a phenotype (e.g., weight, size, shape, color) that can be observed, measured, or compared across organisms or conditions." ; sh:closed true ; - sh:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37007,24 +37153,6 @@ biolink:PhenotypicQuality a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -37032,20 +37160,26 @@ biolink:PhenotypicQuality a sh:NodeShape ; sh:order 13 ; sh:path biolink:category ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 12 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -37059,92 +37193,73 @@ biolink:PhenotypicQuality a sh:NodeShape ; sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; - sh:targetClass biolink:PhenotypicQuality . - -biolink:PhenotypicSex a sh:NodeShape ; - sh:closed true ; - sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path biolink:information_content ] ; + sh:targetClass biolink:PhenotypicQuality . + +biolink:PhenotypicSex a sh:NodeShape ; + rdfs:comment "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37152,11 +37267,23 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:taxon ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -37169,13 +37296,17 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:information_content ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -37183,99 +37314,134 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:order 0 ; sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ] ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ] ; sh:targetClass biolink:PhenotypicSex . biolink:PhysicalEssence a sh:NodeShape ; + rdfs:comment "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." ; sh:closed false ; - sh:description "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:PhysicalEssence . biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; + rdfs:comment "Either a physical or processual entity." ; sh:closed false ; - sh:description "Either a physical or processual entity." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:PhysicalEssenceOrOccurrent . biolink:PhysiologicalProcess a sh:NodeShape ; + rdfs:comment "A biological or chemical function within a living organism." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 19 ; + sh:path biolink:deprecated ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], + sh:order 12 ; + sh:path biolink:taxon ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:information_content ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 17 ; + sh:path dct:description ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -37293,34 +37459,28 @@ biolink:PhysiologicalProcess a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ] ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:PhysiologicalProcess . biolink:PlanetaryEntity a sh:NodeShape ; + rdfs:comment "Any entity or process that exists at the level of the whole planet" ; sh:closed true ; - sh:description "Any entity or process that exists at the level of the whole planet" ; - sh:ignoredProperties ( rdf:type biolink:latitude biolink:timepoint biolink:longitude ) ; + sh:ignoredProperties ( rdf:type biolink:longitude biolink:latitude biolink:timepoint ) ; sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37334,23 +37494,23 @@ biolink:PlanetaryEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -37358,76 +37518,87 @@ biolink:PlanetaryEntity a sh:NodeShape ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:equivalent_identifiers ] ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:PlanetaryEntity . biolink:Plant a sh:NodeShape ; sh:closed true ; - sh:description "" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -37435,28 +37606,11 @@ biolink:Plant a sh:NodeShape ; sh:order 4 ; sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37464,43 +37618,50 @@ biolink:Plant a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; @@ -37509,21 +37670,37 @@ biolink:Plant a sh:NodeShape ; sh:targetClass biolink:Plant . biolink:Polypeptide a sh:NodeShape ; + rdfs:comment "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; sh:closed true ; - sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -37531,109 +37708,128 @@ biolink:Polypeptide a sh:NodeShape ; sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:id ] ; + sh:targetClass biolink:Polypeptide . + +biolink:PopulationToPopulationAssociation a sh:NodeShape ; + rdfs:comment "An association between a two populations" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:Polypeptide . - -biolink:PopulationToPopulationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a two populations" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationContentEntity ; + sh:order 46 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that form the subject of the association" ; sh:maxCount 1 ; @@ -37641,50 +37837,73 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:has_confidence_score ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -37692,16 +37911,24 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:order 45 ; sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that form the object of the association" ; sh:maxCount 1 ; @@ -37709,48 +37936,23 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; @@ -37758,212 +37960,184 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path biolink:original_predicate ] ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ] ; sh:targetClass biolink:PopulationToPopulationAssociation . biolink:PosttranslationalModification a sh:NodeShape ; + rdfs:comment "A chemical modification of a polypeptide or protein that occurs after translation, altering its structure, activity, localization, or interactions." ; sh:closed true ; - sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37972,50 +38146,51 @@ biolink:PosttranslationalModification a sh:NodeShape ; sh:order 9 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ] ; + sh:order 8 ; + sh:path biolink:taxon ] ; sh:targetClass biolink:PosttranslationalModification . biolink:PreprintPublication a sh:NodeShape ; + rdfs:comment "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; sh:closed true ; - sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:order 20 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -38023,136 +38198,130 @@ biolink:PreprintPublication a sh:NodeShape ; sh:order 12 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 18 ; + sh:path biolink:iri ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 17 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:taxon ] ; + sh:path biolink:taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ] ; sh:targetClass biolink:PreprintPublication . biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; + rdfs:comment "Describes a regulatory relationship between two genes or gene products." ; sh:closed true ; - sh:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -38160,57 +38329,57 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:class biolink:BiologicalProcess ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -38218,271 +38387,227 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:order 21 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:class biolink:BiologicalProcess ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:regulates ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:BiologicalProcess ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:BiologicalProcess ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:update_date ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:ProcessRegulatesProcessAssociation . - -biolink:ProcessedMaterial a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:provided_by ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:has_attribute ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path rdfs:label ], + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:order 41 ; sh:path biolink:id ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; - sh:order 9 ; - sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path rdf:type ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:subject_feature_name ] ; + sh:targetClass biolink:ProcessRegulatesProcessAssociation . + +biolink:ProcessedMaterial a sh:NodeShape ; + rdfs:comment "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -38495,137 +38620,163 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:chembl_availability_type ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a chemical entity is a natural product." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:chembl_natural_product ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; + sh:order 9 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:xref ], + sh:order 17 ; + sh:path biolink:xref ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:taxon ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:string ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:chembl_prodrug ], - [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:chembl_drug_warning ], + sh:order 29 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Tern indicating the chirality of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:chembl_chirality ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:full_name ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 11 ; + sh:path biolink:chembl_black_box_warning ], + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a chemical entity is a natural product." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:taxon ], + sh:order 12 ; + sh:path biolink:chembl_natural_product ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:has_attribute ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 26 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:full_name ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:chembl_black_box_warning ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:chembl_prodrug ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:iri ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:deprecated ] ; + sh:order 15 ; + sh:path biolink:chembl_drug_warning ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ProcessedMaterial . biolink:Protein a sh:NodeShape ; + rdfs:comment "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:closed true ; - sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -38638,22 +38789,17 @@ biolink:Protein a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:information_content ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -38661,92 +38807,88 @@ biolink:Protein a sh:NodeShape ; sh:order 3 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Protein . - -biolink:ProteinDomain a sh:NodeShape ; - sh:closed true ; - sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 9 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:taxon ] ; + sh:targetClass biolink:Protein . + +biolink:ProteinDomain a sh:NodeShape ; + rdfs:comment "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -38754,66 +38896,23 @@ biolink:ProteinDomain a sh:NodeShape ; sh:order 15 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ProteinDomain . - -biolink:ProteinFamily a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path biolink:id ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; @@ -38825,77 +38924,141 @@ biolink:ProteinFamily a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:ProteinDomain . + +biolink:ProteinFamily a sh:NodeShape ; + rdfs:comment "A set of proteins coding for diverse functions which, by virtue of their high degree of sequence similarity, are believed to have evolved from a single ancestral gene." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:information_content ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], + sh:order 8 ; + sh:path biolink:information_content ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -38903,61 +39066,98 @@ biolink:ProteinFamily a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ] ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:ProteinFamily . biolink:ProteinIsoform a sh:NodeShape ; + rdfs:comment "Represents a protein that is a specific isoform of the canonical or reference protein." ; sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; @@ -38965,27 +39165,12 @@ biolink:ProteinIsoform a sh:NodeShape ; sh:order 7 ; sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -38993,73 +39178,72 @@ biolink:ProteinIsoform a sh:NodeShape ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ] ; + sh:order 13 ; + sh:path rdfs:label ] ; sh:targetClass biolink:ProteinIsoform . biolink:RNAProduct a sh:NodeShape ; + rdfs:comment "High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds typically synthesized by a DNA- or RNA-dependent RNA polymerase that constitutes the product of a gene. Distinct in emphasis from `biolink:Transcript`, which denotes the informational output of transcription at the gene-model level rather than the chemical species itself." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -39068,372 +39252,288 @@ biolink:RNAProduct a sh:NodeShape ; sh:order 9 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ] ; + sh:order 8 ; + sh:path biolink:taxon ] ; sh:targetClass biolink:RNAProduct . biolink:RNAProductIsoform a sh:NodeShape ; + rdfs:comment "Represents a protein that is a specific isoform of the canonical or reference RNA" ; sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:information_content ] ; sh:targetClass biolink:RNAProductIsoform . biolink:ReactionToCatalystAssociation a sh:NodeShape ; + rdfs:comment "A specialization of reaction-to-participant association in which the participant is a gene or gene product (e.g., an enzyme) that catalyses the reaction." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:MolecularEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 22 ; + sh:path biolink:original_object ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 45 ; + sh:path biolink:id ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], + sh:order 34 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:order 14 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:sources ], + sh:order 4 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], + sh:order 46 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:species_context_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:class biolink:MolecularEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:evidence_count ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path dct:description ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 31 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 12 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], + sh:order 40 ; + sh:path biolink:update_date ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:order 52 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], + sh:order 11 ; + sh:path biolink:sources ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -39441,167 +39541,137 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 5 ; sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:deprecated ], + sh:order 50 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 32 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 21 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_feature_name ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:update_date ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 51 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "the side of a reaction being modeled (ie: left or right)" ; sh:in ( "left" "right" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:reaction_side ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 17 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:supporting_text ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 44 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:deprecated ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; @@ -39609,242 +39679,354 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:order 24 ; sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 49 ; + sh:path rdfs:label ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:elevate_to_prediction ], + sh:order 43 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; + sh:order 33 ; + sh:path biolink:subject_label_closure ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + rdfs:comment "An association between a biochemical reaction and a participating molecular entity, qualified by the stoichiometry, the side (reactant vs. product) on which the participant appears, and the direction of the reaction." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 51 ; sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path rdfs:label ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:sources ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 23 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:sources ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], + sh:order 31 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 38 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:update_date ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path dct:description ], + sh:order 34 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], + sh:order 14 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ], [ sh:class biolink:OrganismTaxon ; sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; + sh:order 47 ; + sh:path biolink:category ], + [ sh:class biolink:MolecularEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 13 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:category ], + sh:order 41 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_feature_name ], + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:integer ; sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:stoichiometry ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:evidence_count ], + sh:order 20 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:id ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path rdf:predicate ], + sh:order 21 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:MolecularEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], + sh:order 43 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:iri ] ; + sh:order 50 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ] ; sh:targetClass biolink:ReactionToParticipantAssociation . biolink:ReagentTargetedGene a sh:NodeShape ; + rdfs:comment "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; sh:closed true ; - sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -39859,11 +40041,11 @@ biolink:ReagentTargetedGene a sh:NodeShape ; sh:order 14 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -39871,183 +40053,183 @@ biolink:ReagentTargetedGene a sh:NodeShape ; sh:order 10 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:information_content ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:equivalent_identifiers ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:ReagentTargetedGene . biolink:RegulatoryRegion a sh:NodeShape ; + rdfs:comment "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; sh:closed true ; - sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:RegulatoryRegion . biolink:RelationshipQuantifier a sh:NodeShape ; + rdfs:comment "A mixin for quantifying aspects of the strength, frequency, or specificity of a relationship between two entities." ; sh:closed false ; - sh:ignoredProperties ( biolink:has_total biolink:has_quotient rdf:type biolink:has_percentage biolink:has_count ) ; + sh:ignoredProperties ( biolink:has_count biolink:has_percentage biolink:has_total rdf:type biolink:has_quotient ) ; sh:targetClass biolink:RelationshipQuantifier . biolink:RelationshipType a sh:NodeShape ; + rdfs:comment "An OWL property used as an edge label" ; sh:closed true ; - sh:description "An OWL property used as an edge label" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; @@ -40059,19 +40241,26 @@ biolink:RelationshipType a sh:NodeShape ; sh:targetClass biolink:RelationshipType . biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; + rdfs:comment "A result of a relative frequency analysis." ; sh:closed true ; - sh:description "A result of a relative frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -40079,163 +40268,226 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:RelativeFrequencyAnalysisResult . biolink:SensitivityQuantifier a sh:NodeShape ; + rdfs:comment "A relationship quantifier that measures the sensitivity of a relationship, such as the proportion of true positives correctly identified in a diagnostic or association context." ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:SensitivityQuantifier . biolink:SequenceAssociation a sh:NodeShape ; + rdfs:comment "An association between a sequence feature and a nucleic acid entity it is localized to." ; sh:closed true ; - sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; - sh:ignoredProperties ( biolink:strand biolink:phase rdf:type biolink:end_interbase_coordinate biolink:start_interbase_coordinate biolink:genome_build ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:ignoredProperties ( biolink:start_interbase_coordinate biolink:phase biolink:strand rdf:type biolink:genome_build biolink:end_interbase_coordinate ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -40243,321 +40495,214 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:SequenceAssociation . - -biolink:SequenceFeatureRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "For example, a particular exon is part of a particular transcript or gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ] ; + sh:targetClass biolink:SequenceAssociation . + +biolink:SequenceFeatureRelationship a sh:NodeShape ; + rdfs:comment "For example, a particular exon is part of a particular transcript or gene" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -40565,203 +40710,294 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:class biolink:Study ; sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 41 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:SequenceFeatureRelationship . + +biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; + rdfs:comment "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Treatment ; + sh:description "treatment whose efficacy is modulated by the subject variant" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ] ; - sh:targetClass biolink:SequenceFeatureRelationship . - -biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -40769,324 +41005,273 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:order 48 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], + [ sh:class biolink:SequenceVariant ; + sh:description "variant that modulates the treatment of some disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:supporting_text ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ] ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . biolink:Serial a sh:NodeShape ; + rdfs:comment "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:closed true ; - sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:taxon ], + sh:order 23 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:order 6 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:equivalent_identifiers ], + sh:order 5 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:summary ], + sh:order 15 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], + sh:order 25 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:volume ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:category ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:format ], + sh:order 9 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:iri ], + sh:order 24 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -41099,110 +41284,110 @@ biolink:Serial a sh:NodeShape ; sh:order 18 ; sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:issue ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path rdf:type ], + sh:order 19 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:volume ], + sh:order 16 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:type ], + sh:order 4 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:rights ], + sh:order 2 ; + sh:path biolink:issue ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:license ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Serial . biolink:SeverityValue a sh:NodeShape ; + rdfs:comment "describes the severity of a phenotypic feature or disease" ; sh:closed true ; - sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], - [ sh:class biolink:QuantityValue ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -41216,33 +41401,27 @@ biolink:SeverityValue a sh:NodeShape ; sh:order 0 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -41250,74 +41429,95 @@ biolink:SeverityValue a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:information_content ] ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ] ; sh:targetClass biolink:SeverityValue . biolink:SiRNA a sh:NodeShape ; + rdfs:comment "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:closed true ; - sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -41325,208 +41525,174 @@ biolink:SiRNA a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ] ; + sh:order 5 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; + rdfs:comment "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:closed true ; - sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a chemical entity is a natural product." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:chembl_natural_product ], - [ sh:datatype xsd:string ; sh:description "Text indicating the availability type of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:chembl_availability_type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_metabolite ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:chembl_drug_warning ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 4 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a chemical entity is a natural product." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:chembl_natural_product ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:trade_name ], + sh:order 21 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:is_toxic ], + sh:order 0 ; + sh:path biolink:is_metabolite ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:category ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 3 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:has_attribute ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; sh:order 7 ; sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:information_content ], + sh:order 5 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path rdfs:label ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_chemical_role ], + sh:order 13 ; + sh:path biolink:chembl_drug_warning ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:chembl_prodrug ], + sh:order 2 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; @@ -41539,70 +41705,96 @@ biolink:SmallMolecule a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:chembl_chirality ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 3 ; - sh:path biolink:available_from ] ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:chembl_prodrug ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:SmallMolecule . biolink:Snv a sh:NodeShape ; + rdfs:comment "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; sh:closed true ; - sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "HGVS syntax refers to the specific rules and conventions used by the Human Variant Nomenclature Committee to describe the location and change in DNA, RNA, and protein sequence variants. This slot is used to capture all the different forms of HGVS nomenclature that may be used to describe a sequence variant, including genomic, transcript, and protein HGVS expressions/nomenclatures and is thus multivalued." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:hgvs_nomenclature ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdf:type ], + sh:order 14 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 17 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -41610,17 +41802,32 @@ biolink:Snv a sh:NodeShape ; sh:order 13 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The state of the sequence w.r.t a reference sequence" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -41633,68 +41840,70 @@ biolink:Snv a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The state of the sequence w.r.t a reference sequence" ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "HGVS syntax refers to the specific rules and conventions used by the Human Variant Nomenclature Committee to describe the location and change in DNA, RNA, and protein sequence variants. This slot is used to capture all the different forms of HGVS nomenclature that may be used to describe a sequence variant, including genomic, transcript, and protein HGVS expressions/nomenclatures and is thus multivalued." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:hgvs_nomenclature ], + sh:order 12 ; + sh:path biolink:taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Snv . biolink:SocioeconomicExposure a sh:NodeShape ; + rdfs:comment "A socioeconomic exposure is a factor relating to social and financial status of an affected individual." ; sh:closed true ; - sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; + sh:order 23 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:exposure_duration ], + sh:order 17 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; + sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:exposure_additional_condition ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:exposure_type ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:exposure_end_age ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -41706,28 +41915,51 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], + sh:order 19 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:exposure_magnitude ], + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:integer ; + sh:description "Starting age of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:exposure_start_age ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:category ], + [ sh:class biolink:SocioeconomicAttribute ; + sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:xref ], + [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:taxon ], + sh:order 6 ; + sh:path biolink:exposure_duration ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; @@ -41735,52 +41967,24 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:order 15 ; sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:exposure_type ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:SocioeconomicAttribute ; - sh:description "connects any entity to an attribute" ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:exposure_magnitude ], [ sh:datatype xsd:string ; sh:description "Route of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:exposure_route ], - [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:string ; - sh:description "Type of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:exposure_vehicle ], - [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_end_age ], [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:exposure_additional_condition ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -41788,119 +41992,59 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:order 21 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:category ] ; + sh:order 2 ; + sh:path biolink:exposure_vehicle ] ; sh:targetClass biolink:SocioeconomicExposure . biolink:SocioeconomicOutcome a sh:NodeShape ; + rdfs:comment "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event" ; sh:closed true ; - sh:description "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event" ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:SocioeconomicOutcome . biolink:SpecificityQuantifier a sh:NodeShape ; + rdfs:comment "A relationship quantifier that measures the specificity of a relationship, such as the proportion of true negatives correctly identified in a diagnostic or association context." ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:SpecificityQuantifier . biolink:StudyPopulation a sh:NodeShape ; + rdfs:comment "A group of people banded together or treated as a group as participants in a research study." ; sh:closed true ; - sh:description "A group of people banded together or treated as a group as participants in a research study." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -41911,272 +42055,264 @@ biolink:StudyPopulation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:StudyPopulation . - -biolink:StudyVariable a sh:NodeShape ; - sh:closed true ; - sh:description "a variable that is used as a measure in the investigation of a study" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 12 ; sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:rights ], + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:StudyPopulation . + +biolink:StudyVariable a sh:NodeShape ; + rdfs:comment "a variable that is used as a measure in the investigation of a study" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], + sh:order 15 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], + sh:order 16 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:information_content ] ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ] ; sh:targetClass biolink:StudyVariable . biolink:SubjectOfInvestigation a sh:NodeShape ; + rdfs:comment "An entity that has the role of being studied in an investigation, study, or experiment" ; sh:closed false ; - sh:description "An entity that has the role of being studied in an investigation, study, or experiment" ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:SubjectOfInvestigation . biolink:TaxonToTaxonAssociation a sh:NodeShape ; + rdfs:comment "An association between two organism taxa, capturing ecological or evolutionary relationships between the taxa (e.g., a host-pathogen relationship or shared habitat)." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:property [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 43 ; + sh:path biolink:category ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -42184,264 +42320,328 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:order 48 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OrganismTaxon ; + sh:description "An association between individuals of different taxa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 7 ; + sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 44 ; + sh:path rdf:type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:TaxonToTaxonAssociation . - -biolink:TextMiningStudyResult a sh:NodeShape ; - sh:closed true ; - sh:description "A study result that represents information extracted from text using natural language processing techniques. This includes the extracted text, location offsets within the source document, confidence scores, and other metadata related to the text mining process." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:subject_location_in_text ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:path rdf:subject ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "The document type (e.g., Journal Article, Case Study, Preprint) for the supporting document used in a Text Mining Result." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:supporting_document_type ], - [ sh:datatype xsd:string ; + sh:order 45 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:TaxonToTaxonAssociation . + +biolink:TextMiningStudyResult a sh:NodeShape ; + rdfs:comment "A study result that represents information extracted from text using natural language processing techniques. This includes the extracted text, location offsets within the source document, confidence scores, and other metadata related to the text mining process." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:integer ; + sh:description "Character offsets for the text span(s) in the supporting text corresponding to the object concept of the extracted assertion" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:object_location_in_text ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 12 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "The document type (e.g., Journal Article, Case Study, Preprint) for the supporting document used in a Text Mining Result." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 4 ; + sh:path biolink:supporting_document_type ], + [ sh:datatype xsd:integer ; + sh:description "Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:subject_location_in_text ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:extraction_confidence_score ], + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The section of the supporting text of a Text Mining Result within the supporting document. This is in the form of the name of the document section (e.g., Abstract, Introduction) that contains the supporting text." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:supporting_text_section_type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The section of the supporting text of a Text Mining Result within the supporting document. This is in the form of the name of the document section (e.g., Abstract, Introduction) that contains the supporting text." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:supporting_text_section_type ], + sh:order 11 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], - [ sh:datatype xsd:integer ; - sh:description "Character offsets for the text span(s) in the supporting text corresponding to the object concept of the extracted assertion" ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_location_in_text ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:extraction_confidence_score ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:information_content ], + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:integer ; sh:description "The document year (typically the publication year) for the supporting document used in a Text Mining Result." ; sh:maxCount 1 ; @@ -42451,100 +42651,99 @@ biolink:TextMiningStudyResult a sh:NodeShape ; sh:targetClass biolink:TextMiningStudyResult . biolink:ThingWithTaxon a sh:NodeShape ; + rdfs:comment "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; sh:closed false ; - sh:description "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:ThingWithTaxon . biolink:TranscriptToGeneRelationship a sh:NodeShape ; + rdfs:comment "A gene is a collection of transcripts" ; sh:closed true ; - sh:description "A gene is a collection of transcripts" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:integer ; sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -42552,39 +42751,44 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:order 16 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 20 ; + sh:path biolink:object_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; @@ -42597,39 +42801,44 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:order 13 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -42637,64 +42846,81 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:Transcript ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -42702,90 +42928,46 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ] ; + sh:order 46 ; + sh:path dct:description ] ; sh:targetClass biolink:TranscriptToGeneRelationship . biolink:TranscriptionFactorBindingSite a sh:NodeShape ; + rdfs:comment "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; sh:closed true ; - sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:information_content ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -42797,729 +42979,901 @@ biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], + sh:order 9 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 15 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ] ; sh:targetClass biolink:TranscriptionFactorBindingSite . biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association in which a sequence variant serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 43 ; + sh:path biolink:category ], [ sh:class biolink:RetrievalSource ; sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:anyURI ; + sh:description "The relationship to the disease" ; + sh:in ( biolink:model_of ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 52 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "The relationship to the disease" ; + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 52 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:nodeKind sh:IRI ; + sh:order 54 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 50 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:SequenceVariant ; + sh:description "A variant that has a role in modeling the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 49 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 53 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 34 ; + sh:path biolink:supporting_text ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 55 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . + +biolink:VariantToDiseaseAssociation a sh:NodeShape ; + rdfs:comment "An association between a sequence variant and a disease, in which the allele state of the variant is linked to the disease state." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 49 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 54 ; sh:path biolink:disease_context_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "E.g. is pathogenic for" ; + sh:in ( biolink:related_condition ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ] ; - sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . - -biolink:VariantToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], [ sh:class biolink:InformationContentEntity ; sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 55 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 42 ; + sh:path biolink:iri ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 52 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:has_confidence_score ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; - sh:order 52 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 53 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:qualified_predicate ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 50 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ] ; + sh:targetClass biolink:VariantToDiseaseAssociation . + +biolink:VariantToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:VariantToEntityAssociationMixin . + +biolink:VariantToGeneAssociation a sh:NodeShape ; + rdfs:comment "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; + sh:closed true ; + sh:ignoredProperties ( biolink:expression_site rdf:type biolink:stage_qualifier biolink:quantifier_qualifier biolink:phenotypic_state ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 54 ; - sh:path biolink:disease_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:anyURI ; - sh:description "E.g. is pathogenic for" ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:condition_associated_with_gene biolink:gene_associated_with_condition biolink:genetically_associated_with ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 55 ; - sh:path biolink:frequency_qualifier ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ] ; - sh:targetClass biolink:VariantToDiseaseAssociation . - -biolink:VariantToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 43 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; @@ -43527,437 +43881,336 @@ biolink:VariantToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:VariantToEntityAssociationMixin . - -biolink:VariantToGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; - sh:ignoredProperties ( biolink:quantifier_qualifier biolink:stage_qualifier biolink:phenotypic_state rdf:type biolink:expression_site ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:has_confidence_score ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 48 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:sources ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 37 ; + sh:path biolink:has_confidence_score ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:order 38 ; + sh:path biolink:elevate_to_prediction ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], + sh:order 39 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:VariantToGeneAssociation . + +biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; + rdfs:comment "An association between a variant and expression of a gene (i.e. e-QTL)" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 46 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 52 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:order 48 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 12 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 32 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 36 ; sh:path biolink:p_value ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 42 ; sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; + sh:order 4 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:sources ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 18 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; + sh:order 49 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 31 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 2 ; + sh:path biolink:stage_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:VariantToGeneAssociation . - -biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:evidence_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_feature_name ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:semmed_agreement_count ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], + sh:order 50 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:supporting_text ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:update_date ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 47 ; sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_confidence_score ], + sh:order 23 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -43965,22 +44218,15 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:order 19 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path dct:description ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 34 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -43988,367 +44234,344 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:sources ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdfs:label ], + sh:order 24 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 40 ; + sh:path biolink:update_date ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 25 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:order 39 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], + sh:order 3 ; + sh:path biolink:phenotypic_state ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:in ( biolink:affects biolink:ameliorates_condition biolink:disrupts biolink:exacerbates_condition biolink:has_adverse_event biolink:has_side_effect biolink:regulates ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:elevate_to_prediction ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 44 ; + sh:path biolink:semmed_agreement_count ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; - sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 51 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], + sh:order 13 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ] ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:VariantToGeneExpressionAssociation . biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:comment "An association between a sequence variant and a phenotypic feature, in which the allele state of the variant is linked to the manifestation of the phenotype." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdf:type ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence_of_type ], + sh:order 59 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], + sh:order 58 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 49 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:has_quotient ], + sh:order 46 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sources ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 55 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 37 ; + sh:path biolink:update_date ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path biolink:has_count ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 54 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:update_date ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 38 ; + sh:path biolink:has_confidence_score ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], + sh:order 9 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_feature_name ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 56 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 48 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:elevate_to_prediction ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 57 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 51 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path rdfs:label ], + sh:order 40 ; + sh:path biolink:evidence_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 55 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sources ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:has_total ], + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 53 ; sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 59 ; - sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 20 ; + sh:path biolink:subject_feature_name ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 60 ; - sh:path biolink:frequency_qualifier ], + sh:order 57 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -44356,168 +44579,143 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_feature_name ], - [ sh:datatype xsd:float ; - sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; - sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:has_confidence_score ], + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 43 ; + sh:path biolink:iri ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:semmed_agreement_count ], + sh:order 60 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:supporting_text ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 48 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 58 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:order 42 ; + sh:path biolink:id ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_feature_name ], + sh:order 52 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:order 39 ; + sh:path biolink:elevate_to_prediction ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 56 ; - sh:path biolink:object_aspect_qualifier ] ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . biolink:VariantToPopulationAssociation a sh:NodeShape ; + rdfs:comment "An association between a variant and a population, where the variant has particular frequency in the population" ; sh:closed true ; - sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; + sh:property [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:date ; sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:update_date ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:integer ; - sh:description "number all populations that carry a particular allele, aka allele number" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:retrieval_source_ids ], + sh:order 32 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -44525,17 +44723,16 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "number in object population that carry a particular allele, aka allele count" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_count ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:supporting_text ], + sh:order 49 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -44543,345 +44740,313 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:order 33 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:sources ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:order 35 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path dct:description ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], + sh:order 23 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_feature_name ], + sh:order 29 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 53 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdf:type ], + sh:order 24 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_predicate ], + sh:order 15 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:order 47 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence_of_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 40 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:subject_category_closure ], + sh:order 6 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_object ], + sh:order 28 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 18 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:double ; - sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:integer ; + sh:description "number all populations that carry a particular allele, aka allele number" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_supporting_studies ], + sh:order 4 ; + sh:path biolink:has_total ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:integer ; sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path biolink:semmed_agreement_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_closure ], + sh:order 38 ; + sh:path biolink:adjusted_p_value ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 19 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence_of_type ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_feature_name ], - [ sh:datatype xsd:string ; - sh:description "a point in time" ; + sh:order 21 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:integer ; + sh:description "number in object population that carry a particular allele, aka allele count" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 3 ; + sh:path biolink:has_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 52 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 30 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:sources ], + [ sh:class biolink:SequenceVariant ; + sh:description "an allele that has a certain frequency in a given population" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_confidence_score ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that is observed to have the frequency" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_subject ], + sh:order 25 ; + sh:path biolink:object_feature_name ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category ], - [ sh:class biolink:SequenceVariant ; - sh:description "an allele that has a certain frequency in a given population" ; + sh:order 31 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:double ; + sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:VariantToPopulationAssociation . - -biolink:Vertebrate a sh:NodeShape ; - sh:closed true ; - sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 37 ; + sh:path biolink:p_value ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; + sh:order 52 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that is observed to have the frequency" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:provided_by ], + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 51 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 39 ; + sh:path biolink:supporting_text ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 27 ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:VariantToPopulationAssociation . + +biolink:Vertebrate a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:information_content ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -44889,81 +45054,117 @@ biolink:Vertebrate a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Vertebrate . biolink:Virus a sh:NodeShape ; + rdfs:comment "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:closed true ; - sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:information_content ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -44971,28 +45172,30 @@ biolink:Virus a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], @@ -45005,63 +45208,59 @@ biolink:Virus a sh:NodeShape ; sh:targetClass biolink:Virus . biolink:WebPage a sh:NodeShape ; + rdfs:comment "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; sh:closed true ; - sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + sh:order 21 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:category ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:anyURI ; sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:mesh_terms ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -45069,104 +45268,106 @@ biolink:WebPage a sh:NodeShape ; sh:order 16 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 20 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 18 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], + sh:order 22 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], + sh:order 17 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ] ; + sh:order 10 ; + sh:path biolink:creation_date ] ; sh:targetClass biolink:WebPage . biolink:AffinityMeasurement a sh:NodeShape ; + rdfs:comment "The type of measurement describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the affinity parameter is pIC50 and the affinity value is 8.6. The binary relation, if given, qualifies the affinity as greater than, less than, or equal." ; sh:closed true ; - sh:description "The type of measurement describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the affinity parameter is pIC50 and the affinity value is 8.6. The binary relation, if given, qualifies the affinity as greater than, less than, or equal." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], + [ sh:description "The type of parameter describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the 'affinity parameter' is pIC50. Used in conjunction with the 'affinity' slot, within an 'affinity measurement'." ; + sh:in ( "pIC50" "pEC50" "pAC50" "pXC50" "pKi" "pKon" "pKoff" "pKd" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:affinity_parameter ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -45174,45 +45375,67 @@ biolink:AffinityMeasurement a sh:NodeShape ; sh:order 5 ; sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:description "Qualifies a value context with a mathematical binary relation." ; + sh:in ( "less_than" "equal_to" "greater_than" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_binary_relation ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:information_content ], + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:float ; sh:description "The numerical value describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the affinity is 8.6. Used in conjunction with the affinity parameter slot." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:affinity ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -45220,164 +45443,178 @@ biolink:AffinityMeasurement a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:id ], - [ sh:description "Qualifies a value context with a mathematical binary relation." ; - sh:in ( "less_than" "equal_to" "greater_than" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_binary_relation ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:xref ], - [ sh:description "The type of parameter describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the 'affinity parameter' is pIC50. Used in conjunction with the 'affinity' slot, within an 'affinity measurement'." ; - sh:in ( "pIC50" "pEC50" "pAC50" "pXC50" "pKi" "pKon" "pKoff" "pKd" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:affinity_parameter ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:AffinityMeasurement . biolink:Behavior a sh:NodeShape ; + rdfs:comment "The internally coordinated responses (actions or inactions) of organisms (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], + sh:order 19 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 12 ; + sh:path biolink:taxon ] ; + sh:targetClass biolink:Behavior . + +biolink:BehavioralFeature a sh:NodeShape ; + rdfs:comment "A phenotypic feature which is behavioral in nature." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ] ; - sh:targetClass biolink:Behavior . - -biolink:BehavioralFeature a sh:NodeShape ; - sh:closed true ; - sh:description "A phenotypic feature which is behavioral in nature." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -45386,9 +45623,27 @@ biolink:BehavioralFeature a sh:NodeShape ; sh:order 1 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -45396,27 +45651,11 @@ biolink:BehavioralFeature a sh:NodeShape ; sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; @@ -45429,186 +45668,192 @@ biolink:BehavioralFeature a sh:NodeShape ; sh:order 0 ; sh:path biolink:inheritance ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ] ; + sh:order 4 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:BehavioralFeature . biolink:CellularComponent a sh:NodeShape ; + rdfs:comment "A location in or around a cell" ; sh:closed true ; - sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:taxon ] ; sh:targetClass biolink:CellularComponent . biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; + rdfs:comment "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; sh:closed false ; - sh:description "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:ChemicalEntityOrProteinOrPolypeptide . biolink:ClinicalAttribute a sh:NodeShape ; + rdfs:comment "Attributes relating to a clinical manifestation" ; sh:closed true ; - sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -45616,35 +45861,32 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], + sh:order 13 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -45652,187 +45894,201 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ] ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:ClinicalAttribute . biolink:ClinicalIntervention a sh:NodeShape ; + rdfs:comment "A medical procedure, treatment, or action taken by healthcare professionals to modify the course of a disease or condition." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], + sh:order 7 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ] ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ClinicalIntervention . biolink:Dataset a sh:NodeShape ; + rdfs:comment "an item that refers to a collection of data from a data source." ; sh:closed true ; - sh:description "an item that refers to a collection of data from a data source." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 15 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:taxon ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -45840,93 +46096,103 @@ biolink:Dataset a sh:NodeShape ; sh:order 6 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ] ; + sh:targetClass biolink:Dataset . + +biolink:DatasetDistribution a sh:NodeShape ; + rdfs:comment "an item that holds distribution level information about a dataset." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 8 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path dct:description ], + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 18 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 15 ; sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Dataset . - -biolink:DatasetDistribution a sh:NodeShape ; - sh:closed true ; - sh:description "an item that holds distribution level information about a dataset." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], + sh:order 19 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A URL from which a specific distribution (serialization or format) of a dataset may be directly downloaded; corresponds to dcat:downloadURL specialised for the dataset distribution domain." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; @@ -45937,21 +46203,12 @@ biolink:DatasetDistribution a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -45965,129 +46222,97 @@ biolink:DatasetDistribution a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:rights ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:iri ] ; + sh:path biolink:taxon ] ; sh:targetClass biolink:DatasetDistribution . biolink:Device a sh:NodeShape ; + rdfs:comment "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:closed true ; - sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:taxon ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -46097,109 +46322,110 @@ biolink:Device a sh:NodeShape ; sh:targetClass biolink:Device . biolink:Exon a sh:NodeShape ; + rdfs:comment "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; sh:closed true ; - sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ] ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Exon . biolink:GeneProductMixin a sh:NodeShape ; + rdfs:comment "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; sh:closed false ; - sh:description "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; @@ -46207,33 +46433,33 @@ biolink:GeneProductMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:synonym ] ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:GeneProductMixin . biolink:OrganismalEntity a sh:NodeShape ; + rdfs:comment "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; sh:closed false ; - sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; - sh:ignoredProperties ( biolink:has_biological_sex rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:ignoredProperties ( rdf:type biolink:has_biological_sex ) ; + sh:property [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -46241,144 +46467,160 @@ biolink:OrganismalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ] ; sh:targetClass biolink:OrganismalEntity . biolink:PredicateMapping a sh:NodeShape ; + rdfs:comment "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:closed true ; - sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:property [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated" ; + sh:in ( "modulation" "allosteric_modulation" "mixed_allosteric_modulation" "biphasic_allosteric_modulation" "mixed_agonism" "positive_modulation" "potentiation" "induction" "cofactor" "activation" "positive_allosteric_modulation" "agonism" "partial_agonism" "biased_agonism" "antibody_agonism" "molecular_channel_opening" "stimulation" "guanyl_nucleotide_exchange" "negative_modulation" "negative_gene_editing_modulation" "gtpase_activation" "atpase_activation" "antisense_oligonucleotide_inhibition" "rna_interference_inhibition" "suppression" "feedback_inhibition" "inhibition" "antibody_inhibition" "antagonism" "allosteric_antagonism" "non_competitive_antagonism" "competitive_inhibition" "noncompetitive_inhibition" "negative_allosteric_modulation" "gating_inhibition" "irreversible_inhibition" "molecular_channel_blockage" "inverse_agonism" "binding" "covalent_binding" "adduction" "crosslinking" "transglutamination" "disuphide_binding" "stabilization" "chaperone_mediated_stabilization" "destabilization" "degradation" "cleavage" "hydrolysis" "disruption" "opening" "multitarget_modulation" "chelation" "release" "sequestration" "oxidoreduction" "exogenous_protein" "exogenous_gene" "transcriptional_regulation" "translational_regulation" "catalytic_activity" "chemical_modification" "relocalization" "isomerization" "signaling_mediated_control" "immune_system_modulation" "vaccine_antigen" "post_transcriptional_regulation" "molecular_modification" "phosphorylation" "dephosphorylation" "neddylation" "deneddylation" "lipidation" "palmitoylation" "myristoylation" "tyrosination" "carboxylation" "ubiquitination" "monoubiquitination" "polyubiquitination" "deubiquitination" "sulfation" "reduction" "oxidation" "acetylation" "deacetylation" "glycosylation" "deglycosylation" "methylation" "trimethylation" "demethylation" "sumoylation" "desumoylation" "ADP-ribosylation" "de-ADP-ribosylation" "ampylation" "hydroxylation" "s_nitrosylation" ) ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "isomerization" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:order 2 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; + sh:description "A qualifier describing the context in which the subject of an association holds." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:object_derivative_qualifier ], + sh:order 6 ; + sh:path biolink:subject_context_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:exact_match ], [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:subject_part_qualifier ], - [ sh:datatype xsd:string ; + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:broad_match ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:narrow_match ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; + sh:description "A qualifier describing the context in which the object of an association holds." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:object_context_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:exact_match ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 11 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; - sh:maxCount 1 ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; @@ -46391,17 +46633,29 @@ biolink:PredicateMapping a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "modulation" "allosteric_modulation" "mixed_allosteric_modulation" "biphasic_allosteric_modulation" "mixed_agonism" "positive_modulation" "potentiation" "induction" "cofactor" "activation" "positive_allosteric_modulation" "agonism" "partial_agonism" "biased_agonism" "antibody_agonism" "molecular_channel_opening" "stimulation" "guanyl_nucleotide_exchange" "negative_modulation" "negative_gene_editing_modulation" "gtpase_activation" "atpase_activation" "antisense_oligonucleotide_inhibition" "rna_interference_inhibition" "suppression" "feedback_inhibition" "inhibition" "antibody_inhibition" "antagonism" "allosteric_antagonism" "non_competitive_antagonism" "competitive_inhibition" "noncompetitive_inhibition" "negative_allosteric_modulation" "gating_inhibition" "irreversible_inhibition" "molecular_channel_blockage" "inverse_agonism" "binding" "covalent_binding" "adduction" "crosslinking" "transglutamination" "disuphide_binding" "stabilization" "chaperone_mediated_stabilization" "destabilization" "degradation" "cleavage" "hydrolysis" "disruption" "opening" "multitarget_modulation" "chelation" "release" "sequestration" "oxidoreduction" "exogenous_protein" "exogenous_gene" "transcriptional_regulation" "translational_regulation" "catalytic_activity" "chemical_modification" "relocalization" "isomerization" "signaling_mediated_control" "immune_system_modulation" "vaccine_antigen" "post_transcriptional_regulation" "molecular_modification" "phosphorylation" "dephosphorylation" "neddylation" "deneddylation" "lipidation" "palmitoylation" "myristoylation" "tyrosination" "carboxylation" "ubiquitination" "monoubiquitination" "polyubiquitination" "deubiquitination" "sulfation" "reduction" "oxidation" "acetylation" "deacetylation" "glycosylation" "deglycosylation" "methylation" "trimethylation" "demethylation" "sumoylation" "desumoylation" "ADP-ribosylation" "de-ADP-ribosylation" "ampylation" "hydroxylation" "s_nitrosylation" ) ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:order 13 ; + sh:path biolink:object_derivative_qualifier ], + [ sh:datatype xsd:string ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it). This qualifier is for the object of an association (or statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:object_part_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:anyURI ; sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; @@ -46410,241 +46664,216 @@ biolink:PredicateMapping a sh:NodeShape ; sh:order 7 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ], - [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ], - [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:object_part_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:species_context_qualifier ] ; + sh:order 0 ; + sh:path biolink:mapped_predicate ] ; sh:targetClass biolink:PredicateMapping . biolink:Procedure a sh:NodeShape ; + rdfs:comment "A series of actions conducted in a certain order or manner" ; sh:closed true ; - sh:description "A series of actions conducted in a certain order or manner" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:Procedure . + +biolink:SocioeconomicAttribute a sh:NodeShape ; + rdfs:comment "Attributes relating to a socioeconomic manifestation" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:has_attribute ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 15 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Procedure . - -biolink:SocioeconomicAttribute a sh:NodeShape ; - sh:closed true ; - sh:description "Attributes relating to a socioeconomic manifestation" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:order 12 ; + sh:path biolink:taxon ], + [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 11 ; + sh:path biolink:information_content ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ] ; + sh:order 0 ; + sh:path rdfs:label ] ; sh:targetClass biolink:SocioeconomicAttribute . biolink:TaxonomicRank a sh:NodeShape ; + rdfs:comment "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)" ; sh:closed true ; - sh:description "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; @@ -46656,20 +46885,44 @@ biolink:TaxonomicRank a sh:NodeShape ; sh:targetClass biolink:TaxonomicRank . biolink:Treatment a sh:NodeShape ; + rdfs:comment "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:closed true ; - sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:synonym ], + sh:order 20 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:full_name ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:exposure_duration ], + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:exposure_end_age ], + [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_procedure ], [ sh:class biolink:Drug ; sh:description "connects an entity to one or more drugs" ; sh:nodeKind sh:IRI ; @@ -46682,456 +46935,410 @@ biolink:Treatment a sh:NodeShape ; sh:order 26 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Type of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_vehicle ], - [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:exposure_magnitude ], + sh:order 24 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 11 ; + sh:path biolink:exposure_additional_condition ], + [ sh:datatype xsd:integer ; + sh:description "Starting age of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:exposure_start_age ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Route of exposure." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:exposure_route ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:iri ], + sh:order 19 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path dct:description ], + sh:order 17 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_procedure ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:exposure_duration ], + sh:order 16 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Additional conditions impacting an exposure event." ; + sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:exposure_additional_condition ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 4 ; + sh:path biolink:exposure_type ], + [ sh:datatype xsd:string ; + sh:description "Route of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:information_content ], + sh:order 6 ; + sh:path biolink:exposure_route ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdf:type ], - [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; + sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:exposure_start_age ], + sh:order 5 ; + sh:path biolink:exposure_vehicle ], [ sh:class biolink:Device ; sh:description "connects an entity to one or more (medical) devices" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_device ], - [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; + [ sh:datatype xsd:string ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:exposure_end_age ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:equivalent_identifiers ], + sh:order 10 ; + sh:path biolink:exposure_magnitude ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:exposure_type ], + sh:order 22 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:Treatment . biolink:Association a sh:NodeShape ; + rdfs:comment "A typed association between two entities, supported by evidence" ; sh:closed true ; - sh:description "A typed association between two entities, supported by evidence" ; - sh:ignoredProperties ( biolink:diseases_confidence_score biolink:object_context_qualifier biolink:stage_qualifier biolink:supporting_documents biolink:qualified_predicate biolink:has_quotient biolink:phenotypic_state rdf:type biolink:dgidb_evidence_score biolink:stoichiometry biolink:interacting_molecules_category biolink:species_context_qualifier biolink:gene2phenotype_confidence_category biolink:object_direction_qualifier biolink:FDA_regulatory_approvals biolink:disease_context_qualifier biolink:genome_build biolink:strand biolink:response_target_context_qualifier biolink:druggable_gene_category biolink:quantifier_qualifier biolink:temporal_context_qualifier biolink:object_derivative_qualifier biolink:max_research_phase biolink:subject_context_qualifier biolink:reaction_side biolink:start_interbase_coordinate biolink:has_count biolink:anatomical_context_qualifier biolink:expression_site biolink:has_affinity biolink:has_total biolink:subject_part_qualifier biolink:object_specialization_qualifier biolink:subject_aspect_qualifier biolink:has_percentage biolink:causal_mechanism_qualifier biolink:end_interbase_coordinate biolink:frequency_qualifier biolink:subject_derivative_qualifier biolink:catalyst_qualifier biolink:clinical_approval_status biolink:population_context_qualifier biolink:response_context_qualifier biolink:subject_form_or_variant_qualifier biolink:FDA_adverse_event_level biolink:associated_environmental_context biolink:subject_specialization_qualifier biolink:dgidb_interaction_score biolink:object_part_qualifier biolink:number_of_cases biolink:reaction_direction biolink:phase biolink:onset_qualifier biolink:object_aspect_qualifier biolink:subject_direction_qualifier biolink:sex_qualifier biolink:allelic_requirement biolink:object_form_or_variant_qualifier biolink:z_score biolink:has_zygosity ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; + sh:ignoredProperties ( biolink:subject_part_qualifier biolink:expression_site biolink:population_context_qualifier biolink:frequency_qualifier biolink:onset_qualifier biolink:has_percentage biolink:catalyst_qualifier biolink:has_total biolink:FDA_regulatory_approvals biolink:associated_environmental_context biolink:genome_build biolink:stage_qualifier biolink:disease_context_qualifier biolink:subject_context_qualifier biolink:z_score biolink:max_research_phase biolink:FDA_adverse_event_level biolink:object_direction_qualifier biolink:has_count biolink:response_target_context_qualifier biolink:has_affinity biolink:qualified_predicate biolink:causal_mechanism_qualifier biolink:object_aspect_qualifier biolink:temporal_context_qualifier rdf:type biolink:object_specialization_qualifier biolink:sex_qualifier biolink:dgidb_interaction_score biolink:start_interbase_coordinate biolink:diseases_confidence_score biolink:subject_specialization_qualifier biolink:dgidb_evidence_score biolink:subject_aspect_qualifier biolink:phase biolink:anatomical_context_qualifier biolink:reaction_direction biolink:object_context_qualifier biolink:interacting_molecules_category biolink:druggable_gene_category biolink:species_context_qualifier biolink:reaction_side biolink:quantifier_qualifier biolink:object_part_qualifier biolink:number_of_cases biolink:end_interbase_coordinate biolink:stoichiometry biolink:allelic_requirement biolink:clinical_approval_status biolink:gene2phenotype_confidence_category biolink:subject_form_or_variant_qualifier biolink:object_form_or_variant_qualifier biolink:subject_derivative_qualifier biolink:object_derivative_qualifier biolink:response_context_qualifier biolink:subject_direction_qualifier biolink:strand biolink:has_zygosity biolink:supporting_documents biolink:phenotypic_state biolink:has_quotient ) ; + sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_feature_name ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:update_date ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The segment of text from a document that supports the mined assertion." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 34 ; + sh:path biolink:supporting_text ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], - [ sh:datatype xsd:integer ; - sh:description "The number of evidence instances that are connected to an association." ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:evidence_count ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:float ; sh:description "connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:has_confidence_score ], + [ sh:class biolink:RetrievalSource ; + sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:sources ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence_of_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Study ; + sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:integer ; + sh:description "The number of evidence instances that are connected to an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:evidence_count ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was updated. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:update_date ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_feature_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence_of_type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:integer ; - sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:semmed_agreement_count ], + sh:order 41 ; + sh:path biolink:id ], + [ sh:class biolink:InformationContentEntity ; + sh:description "Connects an association to detailed information providing supporting evidence." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org)." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:sources ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 46 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "The number of times this concept has been asserted in the SemMedDB literature database." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 40 ; + sh:path biolink:semmed_agreement_count ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating whether a clinical trial finding should be elevated to a prediction." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:elevate_to_prediction ], - [ sh:class biolink:Study ; - sh:description "Studies that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:InformationContentEntity ; - sh:description "Connects an association to detailed information providing supporting evidence." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 44 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "The segment of text from a document that supports the mined assertion." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:supporting_text ], + sh:order 43 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_feature_name ], + sh:order 45 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ] ; + sh:order 20 ; + sh:path biolink:object_feature_name ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "text_co_occurrence" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:Association . biolink:BiologicalEntity a sh:NodeShape ; + rdfs:comment "A heterogeneous substance that contains genomic material or is the product of a biological process." ; sh:closed false ; - sh:ignoredProperties ( biolink:enabled_by biolink:has_gene_or_gene_product biolink:has_biological_sequence biolink:has_gene biolink:has_output rdf:type biolink:has_input biolink:symbol biolink:hgvs_nomenclature biolink:has_biological_sex biolink:inheritance biolink:has_zygosity ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:ignoredProperties ( biolink:enabled_by biolink:hgvs_nomenclature biolink:has_gene_or_gene_product biolink:has_biological_sequence biolink:inheritance biolink:has_output rdf:type biolink:has_zygosity biolink:has_biological_sex biolink:has_gene biolink:symbol biolink:has_input ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -47139,32 +47346,21 @@ biolink:BiologicalEntity a sh:NodeShape ; sh:order 1 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:information_content ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -47176,139 +47372,177 @@ biolink:BiologicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:BiologicalEntity . - -biolink:CellLine a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:taxon ] ; + sh:targetClass biolink:BiologicalEntity . + +biolink:CellLine a sh:NodeShape ; + rdfs:comment "A cultured cell population that is genetically stable and homogeneous, sharing a common propagation history through successive passages in culture." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ] ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:CellLine . biolink:Entity a sh:NodeShape ; + rdfs:comment "Root Biolink Model class for all things and informational relationships, real or imagined." ; sh:closed false ; - sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; - sh:ignoredProperties ( biolink:published_in biolink:ingest_date biolink:object_context_qualifier biolink:full_name biolink:chi_squared_p biolink:clinical_trial_brief_title biolink:elevate_to_prediction biolink:object_feature_name biolink:supporting_document_type biolink:inheritance biolink:gene2phenotype_confidence_category biolink:clinical_trial_primary_purpose biolink:fisher_exact_odds_ratio biolink:format biolink:has_quantitative_value biolink:volume biolink:clinical_trial_age_stage biolink:chembl_chirality biolink:license biolink:resource_role biolink:expression_site biolink:resource_id biolink:has_chemical_role biolink:affinity biolink:object_specialization_qualifier biolink:exposure_end_age dct:type biolink:chembl_prodrug biolink:has_attribute_type biolink:population_context_qualifier biolink:distribution_download_url biolink:clinical_trial_intervention_model biolink:subject_specialization_qualifier biolink:qualifiers biolink:dgidb_interaction_score biolink:has_output biolink:object_part_qualifier biolink:reaction_direction biolink:number_of_cases biolink:phase biolink:subject_direction_qualifier biolink:negated biolink:object_category_closure biolink:max_tolerated_dose biolink:enabled_by biolink:exposure_duration biolink:diseases_confidence_score biolink:exposure_route biolink:has_quotient biolink:clinical_trial_interventions biolink:subject_label_closure biolink:disease_context_qualifier biolink:supporting_text biolink:original_object biolink:extraction_confidence_score biolink:clinical_trial_overall_status biolink:response_target_context_qualifier biolink:druggable_gene_category biolink:affiliation biolink:object_derivative_qualifier biolink:has_gene biolink:original_subject biolink:update_date biolink:subject_context_qualifier biolink:equivalent_identifiers biolink:chi_squared_statistic biolink:chembl_natural_product biolink:primary_knowledge_source biolink:start_interbase_coordinate biolink:has_count biolink:has_evidence biolink:iso_abbreviation biolink:keywords biolink:has_input biolink:timepoint biolink:longitude biolink:in_taxon_label biolink:subject_category biolink:is_toxic biolink:has_device biolink:subject_form_or_variant_qualifier biolink:supporting_document_year biolink:clinical_trial_conditions biolink:log_odds_ratio biolink:exposure_magnitude rdf:object biolink:sex_qualifier biolink:object_form_or_variant_qualifier biolink:rights biolink:stage_qualifier biolink:chembl_availability_type rdf:type biolink:stoichiometry biolink:clinical_trial_enrollment_type biolink:drug_regulatory_status_world_wide biolink:fisher_exact_p biolink:FDA_regulatory_approvals biolink:is_supplement biolink:genome_build biolink:issue biolink:publications biolink:has_gene_or_gene_product biolink:subject_feature_name biolink:upstream_resource_ids biolink:subject_location_in_text biolink:adjusted_p_value biolink:has_drug biolink:trade_name biolink:has_confidence_score biolink:anatomical_context_qualifier biolink:has_affinity biolink:highest_FDA_approval_status biolink:exposure_vehicle biolink:is_metabolite biolink:subject_part_qualifier biolink:chembl_black_box_warning biolink:aggregator_knowledge_source biolink:evidence_count biolink:knowledge_source biolink:sources biolink:has_percentage biolink:xref biolink:frequency_qualifier biolink:catalyst_qualifier biolink:information_content biolink:clinical_approval_status biolink:response_context_qualifier biolink:associated_environmental_context biolink:object_location_in_text biolink:object_category biolink:original_predicate biolink:chi_squared_dof biolink:has_binary_relation biolink:hgvs_nomenclature biolink:has_procedure biolink:agent_type biolink:object_namespace biolink:affinity_parameter biolink:z_score biolink:has_zygosity biolink:knowledge_level biolink:subject_namespace biolink:total_sample_size biolink:chapter biolink:log_odds_ratio_95_ci biolink:qualified_predicate biolink:has_supporting_studies biolink:subject_closure biolink:source_record_urls biolink:clinical_trial_phase biolink:phenotypic_state biolink:supporting_documents biolink:creation_date biolink:dgidb_evidence_score biolink:qualifier biolink:interacting_molecules_category biolink:subject_category_closure biolink:has_study_results biolink:pages biolink:has_taxonomic_rank biolink:clinical_trial_tested_intervention biolink:species_context_qualifier biolink:object_label_closure biolink:authors biolink:in_taxon biolink:provided_by biolink:strand rdf:subject biolink:has_biological_sequence biolink:exposure_start_age biolink:quantifier_qualifier biolink:exposure_type biolink:max_research_phase biolink:temporal_context_qualifier biolink:clinical_trial_start_date rdf:predicate biolink:has_dataset biolink:mesh_terms biolink:has_evidence_of_type biolink:retrieval_source_ids biolink:reaction_side biolink:latitude dct:distribution biolink:supporting_text_section_type biolink:clinical_trial_enrollment biolink:has_total biolink:semmed_agreement_count biolink:taxon biolink:exposure_additional_condition biolink:subject_aspect_qualifier biolink:source_web_page biolink:causal_mechanism_qualifier biolink:end_interbase_coordinate biolink:subject_derivative_qualifier schema1:logo biolink:synonym biolink:available_from biolink:has_qualitative_value biolink:FDA_adverse_event_level biolink:address biolink:clinical_trial_age_range biolink:p_value biolink:onset_qualifier biolink:routes_of_delivery biolink:object_closure biolink:symbol biolink:summary biolink:object_aspect_qualifier biolink:allelic_requirement biolink:object_direction_qualifier biolink:has_biological_sex biolink:chembl_drug_warning ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_attribute ], + sh:ignoredProperties ( biolink:taxon rdf:predicate biolink:catalyst_qualifier biolink:subject_feature_name biolink:has_qualitative_value biolink:equivalent_identifiers biolink:disease_context_qualifier biolink:clinical_trial_start_date biolink:exposure_type biolink:clinical_trial_age_stage biolink:object_feature_name biolink:full_name biolink:object_location_in_text biolink:in_taxon_label biolink:extraction_confidence_score biolink:qualified_predicate biolink:format biolink:affinity biolink:object_specialization_qualifier biolink:issue biolink:timepoint biolink:dgidb_interaction_score biolink:has_gene_or_gene_product biolink:clinical_trial_enrollment biolink:provided_by biolink:dgidb_evidence_score biolink:volume biolink:anatomical_context_qualifier biolink:longitude biolink:druggable_gene_category biolink:update_date biolink:chapter biolink:object_part_qualifier biolink:number_of_cases biolink:has_attribute_type biolink:stoichiometry biolink:clinical_trial_intervention_model biolink:max_tolerated_dose biolink:subject_derivative_qualifier biolink:clinical_trial_overall_status dct:type biolink:p_value biolink:adjusted_p_value biolink:mesh_terms biolink:exposure_magnitude biolink:supporting_documents biolink:enabled_by biolink:supporting_text biolink:subject_part_qualifier biolink:supporting_document_year biolink:keywords biolink:onset_qualifier biolink:is_metabolite biolink:has_procedure biolink:FDA_regulatory_approvals biolink:chi_squared_statistic biolink:associated_environmental_context biolink:negated biolink:affiliation biolink:subject_context_qualifier biolink:symbol biolink:z_score biolink:elevate_to_prediction biolink:original_predicate biolink:clinical_trial_phase biolink:aggregator_knowledge_source biolink:synonym biolink:highest_FDA_approval_status biolink:FDA_adverse_event_level biolink:is_supplement biolink:primary_knowledge_source biolink:retrieval_source_ids biolink:distribution_download_url biolink:exposure_route biolink:exposure_start_age biolink:sources biolink:causal_mechanism_qualifier biolink:publications biolink:temporal_context_qualifier biolink:upstream_resource_ids biolink:resource_id biolink:diseases_confidence_score biolink:rights biolink:subject_aspect_qualifier biolink:subject_category_closure schema1:logo biolink:summary biolink:quantifier_qualifier biolink:in_taxon biolink:allelic_requirement rdf:subject biolink:has_study_results biolink:available_from biolink:has_binary_relation biolink:subject_form_or_variant_qualifier biolink:object_form_or_variant_qualifier biolink:subject_direction_qualifier biolink:chi_squared_dof biolink:trade_name biolink:clinical_trial_conditions biolink:strand biolink:has_zygosity biolink:phenotypic_state biolink:exposure_vehicle biolink:clinical_trial_interventions biolink:population_context_qualifier biolink:has_percentage biolink:has_total biolink:total_sample_size biolink:information_content biolink:source_web_page biolink:license biolink:latitude biolink:source_record_urls biolink:has_biological_sex biolink:semmed_agreement_count biolink:object_category biolink:address rdf:object biolink:has_evidence_of_type biolink:knowledge_source biolink:object_direction_qualifier biolink:iso_abbreviation biolink:has_count biolink:response_target_context_qualifier biolink:has_affinity biolink:qualifiers dct:distribution biolink:exposure_end_age biolink:authors biolink:phase biolink:ingest_date biolink:inheritance biolink:has_supporting_studies biolink:clinical_trial_primary_purpose biolink:clinical_trial_age_range biolink:has_taxonomic_rank biolink:original_subject biolink:interacting_molecules_category biolink:species_context_qualifier biolink:reaction_direction biolink:chembl_chirality biolink:reaction_side biolink:clinical_trial_brief_title biolink:end_interbase_coordinate biolink:chi_squared_p biolink:clinical_approval_status biolink:creation_date biolink:knowledge_level biolink:object_derivative_qualifier biolink:response_context_qualifier biolink:has_chemical_role biolink:clinical_trial_enrollment_type biolink:subject_location_in_text biolink:hgvs_nomenclature biolink:expression_site biolink:resource_role biolink:is_toxic biolink:object_category_closure biolink:published_in biolink:frequency_qualifier biolink:qualifier biolink:exposure_additional_condition biolink:subject_closure biolink:genome_build biolink:stage_qualifier biolink:affinity_parameter biolink:log_odds_ratio_95_ci biolink:supporting_text_section_type biolink:drug_regulatory_status_world_wide biolink:log_odds_ratio biolink:evidence_count biolink:clinical_trial_tested_intervention biolink:routes_of_delivery biolink:max_research_phase biolink:chembl_drug_warning biolink:object_closure biolink:subject_label_closure biolink:has_biological_sequence biolink:has_evidence biolink:supporting_document_type rdf:type biolink:has_quantitative_value biolink:object_aspect_qualifier biolink:sex_qualifier biolink:start_interbase_coordinate biolink:has_dataset biolink:chembl_natural_product biolink:fisher_exact_odds_ratio biolink:has_device biolink:subject_category biolink:xref biolink:agent_type biolink:subject_specialization_qualifier biolink:object_context_qualifier biolink:has_output biolink:has_drug biolink:fisher_exact_p biolink:original_object biolink:exposure_duration biolink:has_input biolink:has_confidence_score biolink:subject_namespace biolink:gene2phenotype_confidence_category biolink:object_label_closure biolink:object_namespace biolink:pages biolink:chembl_black_box_warning biolink:chembl_prodrug biolink:has_gene biolink:chembl_availability_type biolink:has_quotient ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -47316,68 +47550,47 @@ biolink:Entity a sh:NodeShape ; sh:order 5 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:category ] ; + sh:order 4 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Entity . biolink:GeneFamily a sh:NodeShape ; + rdfs:comment "any grouping of multiple genes or gene products related by common descent" ; sh:closed true ; - sh:description "any grouping of multiple genes or gene products related by common descent" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -47388,51 +47601,73 @@ biolink:GeneFamily a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], + sh:order 10 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -47440,70 +47675,95 @@ biolink:GeneFamily a sh:NodeShape ; sh:order 12 ; sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ] ; + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:GeneFamily . biolink:IndividualOrganism a sh:NodeShape ; + rdfs:comment "An instance of an organism. For example, Charles Darwin, my pet cat." ; sh:closed true ; - sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; - sh:ignoredProperties ( biolink:has_biological_sex rdf:type ) ; + sh:ignoredProperties ( rdf:type biolink:has_biological_sex ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:taxon ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:information_content ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -47511,92 +47771,64 @@ biolink:IndividualOrganism a sh:NodeShape ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ] ; + sh:order 16 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:IndividualOrganism . biolink:Outcome a sh:NodeShape ; + rdfs:comment "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological outcomes." ; sh:closed false ; - sh:description "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:Outcome . biolink:StudyResult a sh:NodeShape ; + rdfs:comment "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; sh:closed false ; - sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; - sh:ignoredProperties ( biolink:extraction_confidence_score biolink:total_sample_size biolink:supporting_document_year biolink:log_odds_ratio_95_ci biolink:subject_location_in_text biolink:fisher_exact_odds_ratio biolink:object_location_in_text biolink:chi_squared_p rdf:type biolink:log_odds_ratio biolink:chi_squared_dof biolink:supporting_document_type biolink:chi_squared_statistic biolink:fisher_exact_p biolink:supporting_text_section_type biolink:supporting_text ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:ignoredProperties ( biolink:supporting_text biolink:supporting_document_year biolink:object_location_in_text biolink:fisher_exact_odds_ratio biolink:total_sample_size biolink:chi_squared_dof biolink:chi_squared_statistic biolink:extraction_confidence_score biolink:supporting_document_type rdf:type biolink:log_odds_ratio_95_ci biolink:fisher_exact_p biolink:supporting_text_section_type biolink:subject_location_in_text biolink:log_odds_ratio biolink:chi_squared_p ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 5 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -47604,20 +47836,21 @@ biolink:StudyResult a sh:NodeShape ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -47625,56 +47858,81 @@ biolink:StudyResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:StudyResult . biolink:Transcript a sh:NodeShape ; + rdfs:comment "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:closed true ; - sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -47682,174 +47940,134 @@ biolink:Transcript a sh:NodeShape ; sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:order 4 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Transcript . biolink:Zygosity a sh:NodeShape ; + rdfs:comment "An allelic state describing the degree of similarity between features at a single locus, specifically whether alleles at the same location on paired chromosomes are identical or different." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -47857,58 +48075,59 @@ biolink:Zygosity a sh:NodeShape ; sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:Zygosity . -biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; - sh:closed false ; - sh:description "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProduct . - biolink:Drug a sh:NodeShape ; + rdfs:comment "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; sh:closed true ; - sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + sh:property [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; sh:order 9 ; sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "Tern indicating the chirality of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 14 ; + sh:path biolink:chembl_chirality ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -47916,46 +48135,21 @@ biolink:Drug a sh:NodeShape ; sh:order 23 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:information_content ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:chembl_prodrug ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:is_supplement ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -47967,109 +48161,134 @@ biolink:Drug a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:xref ], + sh:order 10 ; + sh:path biolink:chembl_prodrug ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:description "Text indicating the availability type of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:chembl_drug_warning ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 13 ; + sh:path biolink:chembl_availability_type ], + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a chemical entity is a natural product." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:taxon ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:order 12 ; + sh:path biolink:chembl_natural_product ], [ sh:datatype xsd:string ; sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:chembl_black_box_warning ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + [ sh:datatype xsd:string ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a chemical entity is a natural product." ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:chembl_natural_product ], - [ sh:datatype xsd:string ; + sh:order 18 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path rdf:type ], + sh:order 22 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 1 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Tern indicating the chirality of the chemical entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:chembl_chirality ], + sh:order 27 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Text indicating the availability type of the chemical entity." ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:chembl_availability_type ], + sh:order 15 ; + sh:path biolink:chembl_drug_warning ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_chemical_role ] ; - sh:targetClass biolink:Drug . - -biolink:ExposureEvent a sh:NodeShape ; - sh:closed true ; - sh:description "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; - sh:ignoredProperties ( biolink:has_device biolink:has_gene_or_gene_product biolink:has_biological_sequence biolink:has_quantitative_value biolink:has_drug rdf:type biolink:has_procedure biolink:in_taxon_label biolink:in_taxon ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "Starting age of an exposure event." ; - sh:maxCount 1 ; + sh:path biolink:has_chemical_role ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:exposure_start_age ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], + sh:order 25 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:exposure_magnitude ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 26 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:Drug . + +biolink:ExposureEvent a sh:NodeShape ; + rdfs:comment "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; + sh:closed true ; + sh:ignoredProperties ( biolink:has_gene_or_gene_product biolink:has_biological_sequence biolink:has_device biolink:has_procedure biolink:in_taxon_label rdf:type biolink:has_quantitative_value biolink:has_drug biolink:in_taxon ) ; + sh:property [ sh:datatype xsd:time ; + sh:description "Duration of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:exposure_duration ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path rdf:type ], @@ -48079,87 +48298,105 @@ biolink:ExposureEvent a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:exposure_route ], - [ sh:datatype xsd:string ; - sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 18 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:integer ; - sh:description "Ending stage of an exposure event." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:exposure_end_age ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Type of exposure" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:exposure_type ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:taxon ], + sh:order 23 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "Type of exposure" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:integer ; + sh:description "Ending stage of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:exposure_type ], - [ sh:datatype xsd:time ; - sh:description "Duration of an exposure event." ; + sh:order 5 ; + sh:path biolink:exposure_end_age ], + [ sh:datatype xsd:string ; + sh:description "Type of an exposure event." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:exposure_duration ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:order 2 ; + sh:path biolink:exposure_vehicle ], + [ sh:datatype xsd:string ; + sh:description "Magnitude of an exposure event, e.g, parts per million of a toxic chemical." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:exposure_magnitude ], + [ sh:datatype xsd:integer ; + sh:description "Starting age of an exposure event." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:exposure_start_age ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Could generally be a CURIE from a suitable exposure ontology like ECTO." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Type of an exposure event." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:exposure_vehicle ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 20 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:deprecated ], + sh:order 16 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "Additional conditions impacting an exposure event." ; sh:maxCount 1 ; @@ -48167,44 +48404,57 @@ biolink:ExposureEvent a sh:NodeShape ; sh:order 8 ; sh:path biolink:exposure_additional_condition ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdfs:label ], + sh:order 17 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ] ; + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path dct:description ] ; sh:targetClass biolink:ExposureEvent . biolink:GeneOrGeneProductOrGeneFamily a sh:NodeShape ; + rdfs:comment "A union of gene family or gene loci or gene products, useful to define the association between a gene or gene product or gene family and some other general class of entity." ; sh:closed false ; - sh:description "A union of gene family or gene loci or gene products, useful to define the association between a gene or gene product or gene family and some other general class of entity (e.g. biological process or anatomical entity)" ; sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeneOrGeneProductOrGeneFamily . biolink:MaterialSample a sh:NodeShape ; + rdfs:comment "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; sh:closed true ; - sh:description "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -48212,21 +48462,17 @@ biolink:MaterialSample a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -48234,11 +48480,16 @@ biolink:MaterialSample a sh:NodeShape ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -48246,61 +48497,48 @@ biolink:MaterialSample a sh:NodeShape ; sh:order 6 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; + sh:order 0 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:MaterialSample . biolink:Onset a sh:NodeShape ; + rdfs:comment "The age group in which (disease) symptom manifestations appear." ; sh:closed true ; - sh:description "The age group in which (disease) symptom manifestations appear." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -48313,34 +48551,30 @@ biolink:Onset a sh:NodeShape ; sh:order 10 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], + sh:order 12 ; + sh:path biolink:taxon ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -48348,26 +48582,18 @@ biolink:Onset a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -48375,343 +48601,366 @@ biolink:Onset a sh:NodeShape ; sh:order 3 ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Onset . - -biolink:Pathway a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path dct:description ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:category ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; + sh:targetClass biolink:Onset . + +biolink:Pathway a sh:NodeShape ; + rdfs:comment "A hierarchical ordering of connected molecular reactions (steps) that represent a specific biological process, such as signaling or metabolism." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], + sh:order 12 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:category ], [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ] ; + sh:order 1 ; + sh:path biolink:has_input ] ; sh:targetClass biolink:Pathway . biolink:BiologicalProcess a sh:NodeShape ; + rdfs:comment "One or more causally connected executions of molecular functions" ; sh:closed true ; - sh:description "One or more causally connected executions of molecular functions" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 16 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:category ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:category ], + sh:order 15 ; + sh:path rdf:type ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 12 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ] ; + sh:targetClass biolink:BiologicalProcess . + +biolink:LifeStage a sh:NodeShape ; + rdfs:comment "A stage of development or growth of an organism, including post-natal adult stages" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:iri ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 6 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:BiologicalProcess . - -biolink:LifeStage a sh:NodeShape ; - sh:closed true ; - sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -48722,136 +48971,167 @@ biolink:LifeStage a sh:NodeShape ; sh:targetClass biolink:LifeStage . biolink:NucleicAcidEntity a sh:NodeShape ; + rdfs:comment "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:closed true ; - sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], + sh:property [ sh:datatype xsd:string ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; sh:description "Text describing warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:chembl_drug_warning ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:xref ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; - sh:order 10 ; - sh:path biolink:routes_of_delivery ], + sh:order 30 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Tern indicating the chirality of the chemical entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:chembl_chirality ], + sh:order 24 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:chembl_black_box_warning ], + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path rdf:type ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 28 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Tern indicating the chirality of the chemical entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path biolink:chembl_chirality ], + [ sh:datatype xsd:string ; + sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:chembl_black_box_warning ], [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; + sh:description "Flag indicating if a chemical entity is a natural product." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:chembl_prodrug ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:has_attribute ], + sh:order 13 ; + sh:path biolink:chembl_natural_product ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path dct:description ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:is_metabolite ], + sh:order 8 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a chemical entity is a natural product." ; + sh:order 20 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:chembl_natural_product ], + sh:order 19 ; + sh:path biolink:full_name ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; + sh:order 10 ; + sh:path biolink:routes_of_delivery ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Text indicating the availability type of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:chembl_availability_type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:is_metabolite ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -48863,112 +49143,68 @@ biolink:NucleicAcidEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:trade_name ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:category ] ; + sh:order 11 ; + sh:path biolink:chembl_prodrug ] ; sh:targetClass biolink:NucleicAcidEntity . biolink:BiologicalProcessOrActivity a sh:NodeShape ; - sh:closed true ; - sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + rdfs:comment "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:enabled_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_input ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdf:type ], + sh:order 16 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 17 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_output ], + sh:order 0 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -48976,363 +49212,381 @@ biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:order 5 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + sh:order 12 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_output ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ] ; + sh:order 14 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:BiologicalProcessOrActivity . biolink:Case a sh:NodeShape ; + rdfs:comment "An individual (human) organism that has a patient role in some clinical context." ; sh:closed true ; - sh:description "An individual (human) organism that has a patient role in some clinical context." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:equivalent_identifiers ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:taxon ], [ sh:class biolink:BiologicalSex ; - sh:description "The biological sex of the entity (e.g., male or female) regarding a case description from a phenopacket" ; + sh:description "The biological sex of the entity regarding a case description from a phenopacket" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_biological_sex ], [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ] ; + sh:targetClass biolink:Case . + +biolink:MolecularActivity a sh:NodeShape ; + rdfs:comment "An execution of a molecular function carried out by a gene product or macromolecular complex." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 12 ; sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 1 ; + sh:order 4 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the output for the reaction" ; sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:has_attribute ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Case . - -biolink:MolecularActivity a sh:NodeShape ; - sh:closed true ; - sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:MolecularEntity ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:class biolink:MolecularEntity ; sh:description "A chemical entity that is the input for the reaction" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "The gene product, gene, or complex that catalyzes the reaction" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:enabled_by ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:iri ], + sh:path biolink:iri ] ; + sh:targetClass biolink:MolecularActivity . + +biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; + rdfs:comment "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; + sh:order 9 ; sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the output for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ] ; - sh:targetClass biolink:MolecularActivity . - -biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; - sh:closed true ; - sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -49341,49 +49595,38 @@ biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:path biolink:deprecated ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . +biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; + rdfs:comment "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProduct . + biolink:GeneticInheritance a sh:NodeShape ; + rdfs:comment "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next." ; sh:closed true ; - sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:information_content ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -49392,96 +49635,112 @@ biolink:GeneticInheritance a sh:NodeShape ; sh:order 9 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:taxon ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:order 13 ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeneticInheritance . biolink:MolecularEntity a sh:NodeShape ; + rdfs:comment "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; sh:closed true ; - sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; - sh:ignoredProperties ( biolink:in_taxon_label biolink:has_biological_sequence rdf:type biolink:in_taxon ) ; + sh:ignoredProperties ( biolink:has_biological_sequence rdf:type biolink:in_taxon_label biolink:in_taxon ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:order 24 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 3 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Tern indicating the chirality of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "" ; + sh:order 12 ; + sh:path biolink:chembl_chirality ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:trade_name ], + sh:order 0 ; + sh:path biolink:is_metabolite ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -49490,74 +49749,93 @@ biolink:MolecularEntity a sh:NodeShape ; sh:order 1 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:xref ], [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_metabolite ], - [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:chembl_drug_warning ], + sh:order 27 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Tern indicating the chirality of the chemical entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:chembl_chirality ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_chemical_role ], + sh:order 16 ; + sh:path biolink:full_name ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; + sh:order 7 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:is_toxic ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:information_content ], + sh:order 8 ; + sh:path biolink:chembl_prodrug ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:synonym ], + sh:order 23 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 3 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; sh:description "Text indicating the availability type of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:chembl_availability_type ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a chemical entity is a natural product." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:chembl_natural_product ], + sh:order 21 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -49565,29 +49843,10 @@ biolink:MolecularEntity a sh:NodeShape ; sh:order 22 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:chembl_prodrug ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; @@ -49595,110 +49854,114 @@ biolink:MolecularEntity a sh:NodeShape ; sh:order 9 ; sh:path biolink:chembl_black_box_warning ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; - sh:order 7 ; - sh:path biolink:routes_of_delivery ] ; + sh:order 13 ; + sh:path biolink:chembl_drug_warning ], + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a chemical entity is a natural product." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:chembl_natural_product ] ; sh:targetClass biolink:MolecularEntity . biolink:PhysicalEntity a sh:NodeShape ; + rdfs:comment "An entity that has material reality (a.k.a. physical essence)." ; sh:closed true ; - sh:description "An entity that has material reality (a.k.a. physical essence)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:information_content ] ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ] ; sh:targetClass biolink:PhysicalEntity . biolink:MacromolecularMachineMixin a sh:NodeShape ; + rdfs:comment "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; sh:closed false ; - sh:description "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; - sh:ignoredProperties ( biolink:synonym rdf:type biolink:xref ) ; + sh:ignoredProperties ( rdf:type biolink:xref biolink:synonym ) ; sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -49708,143 +49971,217 @@ biolink:MacromolecularMachineMixin a sh:NodeShape ; sh:targetClass biolink:MacromolecularMachineMixin . biolink:Genotype a sh:NodeShape ; + rdfs:comment "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; sh:closed true ; - sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:equivalent_identifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:information_content ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 16 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 12 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:has_biological_sequence ], [ sh:class biolink:Zygosity ; + sh:description "The zygosity characterising a genotype or nucleic acid entity at a particular locus." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_zygosity ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:synonym ], + sh:path biolink:synonym ] ; + sh:targetClass biolink:Genotype . + +biolink:SequenceVariant a sh:NodeShape ; + rdfs:comment "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "HGVS syntax refers to the specific rules and conventions used by the Human Variant Nomenclature Committee to describe the location and change in DNA, RNA, and protein sequence variants. This slot is used to capture all the different forms of HGVS nomenclature that may be used to describe a sequence variant, including genomic, transcript, and protein HGVS expressions/nomenclatures and is thus multivalued." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:hgvs_nomenclature ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:equivalent_identifiers ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:taxon ], + sh:order 17 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:Genotype . - -biolink:SequenceVariant a sh:NodeShape ; - sh:closed true ; - sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], + sh:order 16 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -49862,90 +50199,84 @@ biolink:SequenceVariant a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:SequenceVariant . + +biolink:Agent a sh:NodeShape ; + rdfs:comment "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:id ], + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The state of the sequence w.r.t a reference sequence" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 12 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 5 ; sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "HGVS syntax refers to the specific rules and conventions used by the Human Variant Nomenclature Committee to describe the location and change in DNA, RNA, and protein sequence variants. This slot is used to capture all the different forms of HGVS nomenclature that may be used to describe a sequence variant, including genomic, transcript, and protein HGVS expressions/nomenclatures and is thus multivalued." ; + sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:hgvs_nomenclature ], + sh:path biolink:address ], + [ sh:datatype xsd:anyURI ; + sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:affiliation ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:equivalent_identifiers ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; + sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 7 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:SequenceVariant . - -biolink:Agent a sh:NodeShape ; - sh:closed true ; - sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; sh:maxCount 1 ; @@ -49953,39 +50284,12 @@ biolink:Agent a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -49993,89 +50297,44 @@ biolink:Agent a sh:NodeShape ; sh:order 8 ; sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; - sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:affiliation ], - [ sh:datatype xsd:string ; - sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:address ], - [ sh:datatype xsd:float ; + sh:order 11 ; + sh:path biolink:category ] ; + sh:targetClass biolink:Agent . + +biolink:PhenotypicFeature a sh:NodeShape ; + rdfs:comment "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual often resulting from the interaction of its genotype with its molecular and physical environment." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 9 ; sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 7 ; sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Agent . - -biolink:PhenotypicFeature a sh:NodeShape ; - sh:closed true ; - sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:class biolink:GeneticInheritance ; sh:description "Connects genetic inheritance to a disease or phenotypic feature, as a node property." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:inheritance ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -50083,41 +50342,29 @@ biolink:PhenotypicFeature a sh:NodeShape ; sh:order 14 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -50130,49 +50377,74 @@ biolink:PhenotypicFeature a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ] ; + sh:order 15 ; + sh:path dct:description ] ; sh:targetClass biolink:PhenotypicFeature . biolink:BiologicalSex a sh:NodeShape ; + rdfs:comment "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved." ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -50180,17 +50452,28 @@ biolink:BiologicalSex a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -50198,105 +50481,69 @@ biolink:BiologicalSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:BiologicalSex . biolink:ChemicalRole a sh:NodeShape ; + rdfs:comment "A role played by the molecular entity or part thereof within a chemical context." ; sh:closed true ; - sh:description "A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:taxon ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -50305,197 +50552,162 @@ biolink:ChemicalRole a sh:NodeShape ; sh:order 1 ; sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:equivalent_identifiers ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:ChemicalRole . - -biolink:ChemicalEntity a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; - sh:ignoredProperties ( biolink:has_biological_sequence biolink:highest_FDA_approval_status biolink:is_metabolite rdf:type biolink:drug_regulatory_status_world_wide biolink:in_taxon_label biolink:is_supplement biolink:in_taxon ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 13 ; sh:path biolink:category ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 8 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; + sh:order 15 ; sh:path dct:description ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; + sh:order 11 ; + sh:path biolink:information_content ] ; + sh:targetClass biolink:ChemicalRole . + +biolink:ChemicalEntity a sh:NodeShape ; + rdfs:comment "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; + sh:closed true ; + sh:ignoredProperties ( biolink:highest_FDA_approval_status biolink:has_biological_sequence biolink:is_metabolite biolink:is_supplement biolink:in_taxon_label rdf:type biolink:drug_regulatory_status_world_wide biolink:in_taxon ) ; + sh:property [ sh:datatype xsd:boolean ; sh:description "Flag indicating if a chemical entity is a natural product." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:chembl_natural_product ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:boolean ; + sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:chembl_prodrug ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "Flag indicating if a drug is a prodrug that is active only after being metabolized by the body." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:chembl_prodrug ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Text describing warnings for use of chemicals as therapeutics." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:chembl_drug_warning ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; - sh:order 5 ; - sh:path biolink:routes_of_delivery ], + sh:order 20 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Tern indicating the chirality of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:chembl_chirality ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "Text describing black box warnings for use of chemicals as therapeutics." ; sh:maxCount 1 ; @@ -50503,182 +50715,192 @@ biolink:ChemicalEntity a sh:NodeShape ; sh:order 7 ; sh:path biolink:chembl_black_box_warning ], [ sh:datatype xsd:string ; - sh:description "Text indicating the availability type of the chemical entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:chembl_availability_type ], - [ sh:datatype xsd:string ; - sh:description "Text describing warnings for use of chemicals as therapeutics." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:chembl_drug_warning ] ; - sh:targetClass biolink:ChemicalEntity . - -biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; - sh:closed true ; - sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 22 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 24 ; sh:path dct:description ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "injection" "intravenous_injection" "subcutaneous_injection" "intramuscular_injection" ) ; + sh:order 5 ; + sh:path biolink:routes_of_delivery ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Text indicating the availability type of the chemical entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 9 ; + sh:path biolink:chembl_availability_type ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 17 ; sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 21 ; sh:path biolink:category ], + [ sh:description "The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum." ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:GeneticInheritance ; - sh:description "Connects genetic inheritance to a disease or phenotypic feature, as a node property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:inheritance ], + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 19 ; sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 15 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:trade_name ] ; + sh:targetClass biolink:ChemicalEntity . + +biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; + rdfs:comment "A disease or an individual phenotypic feature, grouped as a single class to accommodate source vocabularies and assertions that do not distinguish the two. Prefer the more specific subclasses disease or phenotypic feature when the distinction is known." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:GeneticInheritance ; + sh:description "Connects genetic inheritance to a disease or phenotypic feature, as a node property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:inheritance ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeature . - -biolink:Gene a sh:NodeShape ; - sh:closed true ; - sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Symbol for a particular thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:symbol ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:order 1 ; sh:path biolink:id ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:taxon ], + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 11 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:information_content ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; + sh:order 12 ; + sh:path biolink:category ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeature . + +biolink:Gene a sh:NodeShape ; + rdfs:comment "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 9 ; @@ -50694,51 +50916,103 @@ biolink:Gene a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:full_name ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:information_content ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; + sh:order 11 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Symbol for a particular thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:symbol ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:information_content ] ; sh:targetClass biolink:Gene . biolink:QuantityValue a sh:NodeShape ; + rdfs:comment "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; sh:closed true ; - sh:description "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype ; sh:description "connects a quantity value to a unit" ; @@ -50755,9 +51029,9 @@ biolink:QuantityValue a sh:NodeShape ; sh:targetClass biolink:QuantityValue . biolink:GeneOrGeneProduct a sh:NodeShape ; + rdfs:comment "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; sh:closed false ; - sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; - sh:ignoredProperties ( biolink:synonym rdf:type biolink:xref ) ; + sh:ignoredProperties ( rdf:type biolink:xref biolink:synonym ) ; sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -50767,36 +51041,24 @@ biolink:GeneOrGeneProduct a sh:NodeShape ; sh:targetClass biolink:GeneOrGeneProduct . biolink:AnatomicalEntity a sh:NodeShape ; + rdfs:comment "A part of a cellular organism at or above the granularity of a protein complex. This is a grouping class with three concrete subclasses that should be preferred when applicable: \"biolink:Cell\" for whole cells, \"biolink:CellularComponent\" for subcellular and intracellular structures (organelles, membranes, bacterial flagella, etc.), and \"biolink:GrossAnatomcialStructure\" for multicellular parts (tissues, organs, body parts). Excludes viral and other acellular biological entities." ; sh:closed true ; - sh:description "A subcellular location, cell type or gross anatomical part" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -50808,27 +51070,6 @@ biolink:AnatomicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -50836,153 +51077,239 @@ biolink:AnatomicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:taxon ], + sh:order 7 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:AnatomicalEntity . biolink:Disease a sh:NodeShape ; + rdfs:comment "A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury." ; sh:closed true ; - sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:GeneticInheritance ; + sh:description "Connects genetic inheritance to a disease or phenotypic feature, as a node property." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:inheritance ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:information_content ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:Disease . + +biolink:NamedThing a sh:NodeShape ; + rdfs:comment "a databased entity or concept/class" ; + sh:closed true ; + sh:ignoredProperties ( biolink:total_sample_size biolink:source_web_page biolink:license biolink:latitude biolink:has_qualitative_value biolink:source_record_urls biolink:has_biological_sex biolink:clinical_trial_start_date biolink:exposure_type biolink:clinical_trial_age_stage biolink:address biolink:object_location_in_text biolink:iso_abbreviation biolink:in_taxon_label biolink:extraction_confidence_score biolink:format biolink:affinity dct:distribution biolink:exposure_end_age biolink:issue biolink:timepoint biolink:has_gene_or_gene_product biolink:clinical_trial_enrollment biolink:authors biolink:volume biolink:ingest_date biolink:inheritance biolink:clinical_trial_primary_purpose biolink:clinical_trial_age_range biolink:has_taxonomic_rank biolink:longitude biolink:chembl_chirality biolink:chapter biolink:clinical_trial_brief_title biolink:has_attribute_type biolink:chi_squared_p biolink:creation_date biolink:clinical_trial_intervention_model biolink:max_tolerated_dose biolink:clinical_trial_overall_status biolink:has_chemical_role dct:type biolink:clinical_trial_enrollment_type biolink:mesh_terms biolink:exposure_magnitude biolink:subject_location_in_text biolink:enabled_by biolink:supporting_text biolink:hgvs_nomenclature biolink:supporting_document_year biolink:keywords biolink:resource_role biolink:is_toxic biolink:is_metabolite biolink:published_in biolink:has_procedure biolink:chi_squared_statistic biolink:exposure_additional_condition biolink:affiliation biolink:affinity_parameter biolink:log_odds_ratio_95_ci biolink:supporting_text_section_type biolink:symbol biolink:drug_regulatory_status_world_wide biolink:log_odds_ratio biolink:clinical_trial_tested_intervention biolink:routes_of_delivery biolink:clinical_trial_phase biolink:chembl_drug_warning biolink:highest_FDA_approval_status biolink:has_biological_sequence biolink:is_supplement biolink:supporting_document_type biolink:has_quantitative_value rdf:type biolink:distribution_download_url biolink:exposure_route biolink:exposure_start_age biolink:upstream_resource_ids biolink:exposure_vehicle biolink:resource_id biolink:has_dataset biolink:rights biolink:fisher_exact_odds_ratio biolink:chembl_natural_product biolink:has_device biolink:has_output schema1:logo biolink:summary biolink:has_drug biolink:fisher_exact_p biolink:exposure_duration biolink:has_input biolink:in_taxon biolink:has_study_results biolink:available_from biolink:has_binary_relation biolink:pages biolink:chi_squared_dof biolink:chembl_black_box_warning biolink:trade_name biolink:clinical_trial_conditions biolink:has_zygosity biolink:chembl_prodrug biolink:has_gene biolink:chembl_availability_type biolink:clinical_trial_interventions ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:full_name ], + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 3 ; sh:path biolink:synonym ], - [ sh:class biolink:GeneticInheritance ; - sh:description "Connects genetic inheritance to a disease or phenotypic feature, as a node property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:inheritance ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 11 ; sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:information_content ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 16 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Disease . - -biolink:NamedThing a sh:NodeShape ; - sh:closed true ; - sh:description "a databased entity or concept/class" ; - sh:ignoredProperties ( biolink:published_in biolink:ingest_date biolink:chi_squared_p biolink:clinical_trial_brief_title rdf:type biolink:chembl_availability_type biolink:chembl_drug_warning biolink:supporting_document_type biolink:clinical_trial_enrollment_type biolink:drug_regulatory_status_world_wide biolink:inheritance biolink:clinical_trial_primary_purpose biolink:fisher_exact_p biolink:is_supplement biolink:issue biolink:has_gene_or_gene_product biolink:upstream_resource_ids biolink:subject_location_in_text biolink:fisher_exact_odds_ratio biolink:format biolink:has_quantitative_value biolink:has_drug biolink:volume biolink:clinical_trial_age_stage biolink:chembl_chirality biolink:trade_name biolink:license biolink:resource_role biolink:highest_FDA_approval_status biolink:resource_id biolink:is_metabolite biolink:exposure_vehicle biolink:has_chemical_role biolink:chembl_black_box_warning biolink:affinity biolink:exposure_end_age dct:type biolink:chembl_prodrug biolink:has_attribute_type biolink:distribution_download_url biolink:clinical_trial_intervention_model biolink:object_location_in_text biolink:has_output biolink:chi_squared_dof biolink:has_binary_relation biolink:hgvs_nomenclature biolink:has_procedure biolink:affinity_parameter biolink:has_zygosity biolink:max_tolerated_dose biolink:enabled_by biolink:exposure_duration biolink:total_sample_size biolink:chapter biolink:log_odds_ratio_95_ci biolink:exposure_route biolink:source_record_urls biolink:clinical_trial_phase biolink:creation_date biolink:clinical_trial_interventions biolink:has_study_results biolink:pages biolink:has_taxonomic_rank biolink:clinical_trial_tested_intervention biolink:authors biolink:supporting_text biolink:in_taxon biolink:extraction_confidence_score biolink:clinical_trial_overall_status biolink:has_biological_sequence biolink:affiliation biolink:exposure_start_age biolink:exposure_type biolink:has_gene biolink:clinical_trial_start_date biolink:has_dataset biolink:mesh_terms biolink:chi_squared_statistic biolink:chembl_natural_product biolink:latitude dct:distribution biolink:supporting_text_section_type biolink:clinical_trial_enrollment biolink:iso_abbreviation biolink:exposure_additional_condition biolink:source_web_page biolink:keywords biolink:has_input biolink:timepoint biolink:longitude biolink:in_taxon_label schema1:logo biolink:available_from biolink:is_toxic biolink:has_device biolink:has_qualitative_value biolink:supporting_document_year biolink:address biolink:clinical_trial_age_range biolink:clinical_trial_conditions biolink:log_odds_ratio biolink:exposure_magnitude biolink:routes_of_delivery biolink:symbol biolink:summary biolink:rights biolink:has_biological_sex ) ; - sh:property [ sh:datatype xsd:anyURI ; + [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -50990,44 +51317,17 @@ biolink:NamedThing a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -51038,35 +51338,12 @@ biolink:NamedThing a sh:NodeShape ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:equivalent_identifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ] ; + sh:path biolink:equivalent_identifiers ] ; sh:targetClass biolink:NamedThing . biolink:OrganismTaxon a sh:NodeShape ; + rdfs:comment "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; sh:closed true ; - sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; @@ -51074,18 +51351,11 @@ biolink:OrganismTaxon a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:taxon ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -51093,94 +51363,97 @@ biolink:OrganismTaxon a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:information_content ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:provided_by ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:information_content ], + sh:order 3 ; + sh:path biolink:full_name ], [ sh:class biolink:TaxonomicRank ; + sh:description "The taxonomic rank (e.g. species, genus, family, order, kingdom) assigned to an organism taxon." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_taxonomic_rank ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:xref ] ; + sh:order 15 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:OrganismTaxon . biolink:EvidenceType a sh:NodeShape ; + rdfs:comment "Class of evidence that supports an association" ; sh:closed true ; - sh:description "Class of evidence that supports an association" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:float ; + sh:property [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:information_content ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:taxon ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -51188,144 +51461,156 @@ biolink:EvidenceType a sh:NodeShape ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:equivalent_identifiers ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 3 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:taxon ], + sh:order 2 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ] ; sh:targetClass biolink:EvidenceType . biolink:Publication a sh:NodeShape ; + rdfs:comment "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope." ; sh:closed true ; - sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; - sh:ignoredProperties ( biolink:issue biolink:published_in biolink:chapter biolink:iso_abbreviation rdf:type biolink:volume ) ; + sh:ignoredProperties ( biolink:iso_abbreviation biolink:volume biolink:published_in rdf:type biolink:chapter biolink:issue ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:information_content ], + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:taxon ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; + sh:order 22 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -51337,22 +51622,6 @@ biolink:Publication a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -51360,148 +51629,158 @@ biolink:Publication a sh:NodeShape ; sh:order 12 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 17 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:equivalent_identifiers ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:taxon ], + sh:order 18 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:equivalent_identifiers ], + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ] ; + sh:order 9 ; + sh:path biolink:format ] ; sh:targetClass biolink:Publication . biolink:Study a sh:NodeShape ; + rdfs:comment "a detailed investigation and/or analysis" ; sh:closed true ; - sh:description "a detailed investigation and/or analysis" ; - sh:ignoredProperties ( biolink:clinical_trial_intervention_model biolink:clinical_trial_overall_status biolink:clinical_trial_age_range biolink:clinical_trial_conditions biolink:clinical_trial_start_date biolink:clinical_trial_brief_title biolink:clinical_trial_phase rdf:type biolink:creation_date biolink:clinical_trial_interventions biolink:clinical_trial_age_stage biolink:clinical_trial_enrollment_type biolink:clinical_trial_tested_intervention biolink:clinical_trial_primary_purpose biolink:clinical_trial_enrollment ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:ignoredProperties ( biolink:clinical_trial_phase biolink:creation_date biolink:clinical_trial_enrollment biolink:clinical_trial_intervention_model biolink:clinical_trial_overall_status biolink:clinical_trial_enrollment_type biolink:clinical_trial_primary_purpose biolink:clinical_trial_age_range biolink:clinical_trial_conditions biolink:clinical_trial_interventions rdf:type biolink:clinical_trial_start_date biolink:clinical_trial_brief_title biolink:clinical_trial_age_stage biolink:clinical_trial_tested_intervention ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; sh:description "Information content (IC) value for a term, primarily from Automats." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:information_content ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:equivalent_identifiers ], [ sh:class biolink:StudyResult ; sh:description "Connects an study to instances of its study result" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_study_results ], [ sh:datatype xsd:anyURI ; - sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:taxon ], + sh:order 2 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:anyURI ; + sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:Study . biolink:InformationContentEntity a sh:NodeShape ; + rdfs:comment "a piece of information that typically describes some topic of discourse or is used as support." ; sh:closed false ; - sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; - sh:ignoredProperties ( biolink:published_in biolink:ingest_date biolink:chapter biolink:source_record_urls rdf:type biolink:pages biolink:authors biolink:issue biolink:upstream_resource_ids biolink:volume biolink:has_dataset biolink:mesh_terms dct:distribution biolink:resource_role biolink:resource_id biolink:iso_abbreviation dct:type biolink:source_web_page biolink:keywords schema1:logo biolink:distribution_download_url biolink:summary ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], + sh:ignoredProperties ( biolink:keywords biolink:resource_role biolink:published_in biolink:source_web_page biolink:source_record_urls biolink:iso_abbreviation biolink:distribution_download_url rdf:type biolink:upstream_resource_ids dct:distribution biolink:issue biolink:resource_id biolink:has_dataset biolink:authors biolink:volume biolink:ingest_date schema1:logo biolink:summary biolink:chapter biolink:pages dct:type biolink:mesh_terms ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -51509,177 +51788,204 @@ biolink:InformationContentEntity a sh:NodeShape ; sh:order 10 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:equivalent_identifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:equivalent_identifiers ], + sh:order 9 ; + sh:path biolink:information_content ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 16 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; - sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:information_content ], + sh:order 14 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:InformationContentEntity . biolink:RetrievalSource a sh:NodeShape ; + rdfs:comment "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; sh:closed true ; - sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:synonym ], + sh:order 22 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:resource_id ], + sh:order 10 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; + sh:description "A list of upstream InformationResources from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:equivalent_identifiers ], + sh:order 2 ; + sh:path biolink:upstream_resource_ids ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:xref ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:information_content ], + sh:order 8 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "One or more URLs that link to a specific web page or document provided by the InformationResource, that contains a record of the knowledge expressed in the Edge." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 3 ; + sh:path biolink:source_record_urls ], + [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:resource_role ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:license ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:information_content ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A list of upstream InformationResources from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge." ; + [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:upstream_resource_ids ], + sh:order 18 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -51688,129 +51994,121 @@ biolink:RetrievalSource a sh:NodeShape ; sh:order 15 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], - [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; + sh:order 6 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:resource_role ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 0 ; + sh:path biolink:resource_id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "One or more URLs that link to a specific web page or document provided by the InformationResource, that contains a record of the knowledge expressed in the Edge." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:source_record_urls ], + sh:order 19 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdf:type ] ; + sh:order 12 ; + sh:path biolink:equivalent_identifiers ] ; sh:targetClass biolink:RetrievalSource . biolink:Attribute a sh:NodeShape ; + rdfs:comment "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; sh:closed true ; - sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:information_content ], + [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:equivalent_identifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:anyURI ; sh:description "A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology." ; sh:maxCount 1 ; @@ -51818,31 +52116,27 @@ biolink:Attribute a sh:NodeShape ; sh:order 12 ; sh:path biolink:taxon ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:float ; - sh:description "Information content (IC) value for a term, primarily from Automats." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:information_content ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 15 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ] ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; + rdfs:comment "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; sh:closed false ; - sh:description "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; diff --git a/project/shex/biolink_model.shex b/project/shex/biolink_model.shex index 0e99bd31d..e4aeb139b 100644 --- a/project/shex/biolink_model.shex +++ b/project/shex/biolink_model.shex @@ -165,7 +165,8 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie + rdf:predicate [ + ] ) ; rdf:type [ ] ) @@ -176,7 +177,8 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie + rdf:predicate [ + ] ) ; rdf:type [ ] ) @@ -202,7 +204,7 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie + rdf:predicate [ ] ) ; rdf:type [ ] ) @@ -220,10 +222,10 @@ linkml:Sparqlpath xsd:string CLOSED { ( $ ( & ; rdf:type [ ] ? ; - @linkml:Uriorcurie ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? + @ ; + @ ? ; + @ ? ; + @ ? ) ; rdf:type [
] ) @@ -235,18 +237,18 @@ linkml:Sparqlpath xsd:string ( $ ( & ; rdf:type [ ] ? ; rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate @ ; rdf:object @ ; - @linkml:Boolean ? ; - @linkml:String ? ; + @ ? ; + @ ? ; @ * ; @ * ; @ * ; @ * ; @ * ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String * ; + @ ? ; + @ ? ; + @ * ; [ @@ -263,33 +265,33 @@ linkml:Sparqlpath xsd:string ] ; @ ? ; - @linkml:String ? ; - @linkml:Uriorcurie ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? ; + @ ? ; + @ ? ; + @ ? ; + @ ? ; + @ ? ; @ ? ; @ ? ; - @linkml:String * ; - @linkml:String * ; + @ * ; + @ * ; @ * ; @ * ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String * ; - @linkml:String * ; + @ ? ; + @ ? ; + @ * ; + @ * ; @ * ; - @linkml:Float ? ; - @linkml:Float ? ; - @linkml:String * ; + @ ? ; + @ ? ; + @ * ; @ * ; - @linkml:Date ? ; - @linkml:Float ? ; - @linkml:Boolean ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - rdf:type @linkml:String * ; - @linkml:Uriorcurie * + @ ? ; + @ ? ; + @ ? ; + @ ? ; + @ ? ; + rdf:type @ * ; + @ * ) ; rdf:type [ ] ) @@ -373,23 +375,137 @@ linkml:Sparqlpath xsd:string rdf:subject @ ; rdf:object @ ; @ ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:Uriorcurie ? ; + @ ? ; @ ? ; @ ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Double ? ; - @linkml:Double ? + @ ? ; + @ ? ; + @ ? ; + @ ? ) ; rdf:type [ ] ) @@ -484,7 +600,7 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie + rdf:predicate [ ] ) ; rdf:type [ ] ) @@ -495,7 +611,8 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie + rdf:predicate [ + ] ) ; rdf:type [ ] ) @@ -522,7 +639,7 @@ linkml:Sparqlpath xsd:string CLOSED { ( $ ( & ; rdf:type [ ] ? ; - rdf:type @linkml:String * + rdf:type @ * ) ; rdf:type [ ] ) @@ -531,9 +648,9 @@ linkml:Sparqlpath xsd:string CLOSED { ( $ ( & ; rdf:type [ ] ? ; - @linkml:Uriorcurie ; - @linkml:String ? ; - @linkml:String ? + @ ; + @ ? ; + @ ? ) ; rdf:type [ ] ) @@ -564,7 +681,7 @@ linkml:Sparqlpath xsd:string { ( $ ( rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate @ ; rdf:object @ ) ; rdf:type [ ] ? @@ -591,23 +708,137 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; @ ? ; @ ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:Uriorcurie ? ; + @ ? ; @ ? ; @ ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Double ? ; - @linkml:Double ? + @ ? ; + @ ? ; + @ ? ; + @ ? ) ; rdf:type [ ] ) @@ -630,34 +861,91 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; & ; rdf:type [ ] ? ; - @linkml:String ? ; - @linkml:String ? ; - [ - - - ] ? ; - @linkml:String ? ; - @linkml:Uriorcurie ? ; - rdf:subject @ ; - rdf:object @ - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( & ; - rdf:type [ ] ? - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( & ; - rdf:type [ ] ? ; - & ; - rdf:type [ ] ? + @ ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; + [ + + + ] ? ; + @ ? ; + @ ? ; + rdf:subject @ ; + rdf:object @ + ) ; + rdf:type [ ] + ) +} + + CLOSED { + ( $ ( & ; + rdf:type [ ] ? + ) ; + rdf:type [ ] + ) +} + + CLOSED { + ( $ ( & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ) ; rdf:type [ ] ) @@ -672,17 +960,131 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; rdf:subject @ ; @ ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:Uriorcurie ? + @ ? ) ; rdf:type [ ] ) @@ -698,9 +1100,9 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; rdf:subject @ ; @ ? ; - @linkml:Uriorcurie ? ; - @linkml:Uriorcurie ? ; - @linkml:String * + @ ? ; + @ ? ; + @ * ) ; rdf:type [ ] ) @@ -709,7 +1111,7 @@ linkml:Sparqlpath xsd:string { ( $ ( rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate @ ; rdf:object @ ) ; rdf:type [ ] ? @@ -1004,10 +1406,11 @@ linkml:Sparqlpath xsd:string ] ? ; @ * ; - @linkml:Uriorcurie ? ; + [ ] ? ; @ ? ; rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate [ + ] ; rdf:object @ ) ; rdf:type [ ] @@ -1018,9 +1421,9 @@ linkml:Sparqlpath xsd:string CLOSED { ( $ ( & ; rdf:type [ ] ? ; - @linkml:Float ? ; - @linkml:Integer ? ; - @linkml:Uriorcurie * + @ ? ; + @ ? ; + @ * ) ; rdf:type [ ] ) @@ -1038,11 +1441,11 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; & ; rdf:type [ ] ? ; - @linkml:String ? ; + @ ? ; [ ] * ; - @linkml:String ? ; - @linkml:Boolean ? ; + @ ? ; + @ ? ; @ * ; [ @@ -1051,12 +1454,12 @@ linkml:Sparqlpath xsd:string ] * ; - @linkml:Boolean ? ; - @linkml:String ? ; - @linkml:Boolean ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? + @ ? ; + @ ? ; + @ ? ; + @ ? ; + @ ? ; + @ ? ) ; rdf:type [ ] ) @@ -1068,7 +1471,7 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie + rdf:predicate [ ] ) ; rdf:type [ ] ) @@ -1087,7 +1490,7 @@ linkml:Sparqlpath xsd:string ] ? ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate [ ] ; rdf:subject @ ; rdf:object @ ) ; @@ -1105,15 +1508,61 @@ linkml:Sparqlpath xsd:string ( $ ( & ; rdf:type [ ] ? ; @ ? ; - @linkml:String * ; - @linkml:Uriorcurie ? ; + @ * ; + @ ? ; [ ] ? ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie + rdf:predicate [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ) ; rdf:type [ ] ) @@ -1125,7 +1574,7 @@ linkml:Sparqlpath xsd:string @ * ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie + rdf:predicate [ ] ) ; rdf:type [ ] ) @@ -1165,9 +1614,9 @@ linkml:Sparqlpath xsd:string ] ? ; rdf:object @ ; @ ? ; - @linkml:Uriorcurie ? ; - @linkml:Uriorcurie ? ; - @linkml:String * + @ ? ; + @ ? ; + @ * ) ; rdf:type [ ] ) @@ -1179,7 +1628,7 @@ linkml:Sparqlpath xsd:string { ( $ ( rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate @ ; rdf:object @ ) ; rdf:type [ ] ? @@ -1231,7 +1680,7 @@ linkml:Sparqlpath xsd:string ] ? ; [ ] ? ; @ ? ; - @linkml:Uriorcurie ? ; + @ ? ; [ @@ -1414,11 +1863,13 @@ linkml:Sparqlpath xsd:string ] ? ; - @linkml:Float ? ; - @linkml:Integer ? ; + @ ? ; + @ ? ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie + rdf:predicate [ + + ] ) ; rdf:type [ ] ) @@ -1430,7 +1881,7 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; & ; rdf:type [ ] ? ; - @linkml:String ? ; + @ ? ; [ @@ -1485,23 +1936,137 @@ linkml:Sparqlpath xsd:string ] ? ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate [ ] ; @ ? ; - @linkml:Uriorcurie ? ; - @linkml:Uriorcurie ? ; - @linkml:String * ; + @ ? ; + @ ? ; + @ * ; @ ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:Uriorcurie ? + @ ? ) ; rdf:type [ ] ) @@ -1514,23 +2079,137 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; & ; rdf:type [ ] ? ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate [ ] ; @ ? ; - @linkml:Uriorcurie ? ; - @linkml:Uriorcurie ? ; - @linkml:String * ; + @ ? ; + @ ? ; + @ * ; @ ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:Uriorcurie ? + @ ? ) ; rdf:type [ ] ) @@ -1543,43 +2222,159 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; & ; rdf:type [ ] ? ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate [ + + ] ; @ ? ; - @linkml:Uriorcurie ? ; - @linkml:Uriorcurie ? ; - @linkml:String * ; + @ ? ; + @ ? ; + @ * ; @ ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:String ? ; - [ - - - ] ? ; - @linkml:Uriorcurie ? - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( & ; - rdf:type [ ] ? - ) ; - rdf:type [ ] - ) -} - - { - ( $ ( & ; - rdf:type [ ] ? ; - rdf:subject @ - ) ; - rdf:type [ ] ? - ) + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; + [ + + + ] ? ; + @ ? + ) ; + rdf:type [ ] + ) +} + + CLOSED { + ( $ ( & ; + rdf:type [ ] ? + ) ; + rdf:type [ ] + ) +} + + { + ( $ ( & ; + rdf:type [ ] ? ; + rdf:subject @ + ) ; + rdf:type [ ] ? + ) } CLOSED { @@ -1668,8 +2463,8 @@ linkml:Sparqlpath xsd:string ] ? ; - @linkml:String ? ; - @linkml:String ? ; + @ ? ; + @ ? ; [ @@ -1683,18 +2478,18 @@ linkml:Sparqlpath xsd:string ] ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:Integer ? ; + @ ? ; + @ ? ; + @ ? ; + @ ? ; [ ] * ; - @linkml:String ? ; - @linkml:String ? ; + @ ? ; + @ ? ; @ * ; @ * ; - @linkml:Date ? + @ ? ) ; rdf:type [ ] ) @@ -1765,7 +2560,7 @@ linkml:Sparqlpath xsd:string ( $ ( & ; rdf:type [ ] ? ; rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate [ ] ; rdf:object @ ; @ * ) ; @@ -1780,25 +2575,140 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; & ; rdf:type [ ] ? ; - @linkml:Float ? ; - @linkml:Float ? ; - @linkml:String ? ; - @linkml:String ? ; + @ ? ; + @ ? ; + @ ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:String ? ; - @linkml:Uriorcurie ? ; + @ ? ; + @ ? ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate [ + ] ; @ ? ; [ ] ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; @ ? ) ; rdf:type [ ] @@ -1816,7 +2726,7 @@ linkml:Sparqlpath xsd:string CLOSED { ( $ ( & ; rdf:type [ ] ? ; - @linkml:String ? + @ ? ) ; rdf:type [ ] ) @@ -1825,8 +2735,8 @@ linkml:Sparqlpath xsd:string CLOSED { ( $ ( & ; rdf:type [ ] ? ; - @linkml:String ? ; - schema1:logo @linkml:String ? + @ ? ; + schema1:logo @ ? ) ; rdf:type [ ] ) @@ -1836,7 +2746,7 @@ linkml:Sparqlpath xsd:string ( $ ( & ; rdf:type [ ] ? ; @ ? ; - @linkml:String ? ; + @ ? ; dcterms:distribution @ ? ) ; rdf:type [ ] @@ -1878,7 +2788,7 @@ linkml:Sparqlpath xsd:string ] ? ; rdf:subject @ ; rdf:object @ ; - rdf:predicate @linkml:Uriorcurie + rdf:predicate [ ] ) ; rdf:type [ ] ) @@ -1917,7 +2827,7 @@ linkml:Sparqlpath xsd:string { ( $ ( rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate @ ; rdf:object @ ) ; rdf:type [ ] ? @@ -1929,7 +2839,7 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; & ; rdf:type [ ] ? ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate [ ] ; rdf:object @ ) ; rdf:type [ ] @@ -1949,7 +2859,7 @@ linkml:Sparqlpath xsd:string { ( $ ( rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate @ ; rdf:object @ ) ; rdf:type [ ] ? @@ -1980,22 +2890,136 @@ linkml:Sparqlpath xsd:string @ ? ; rdf:subject @ ; rdf:object @ ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Double ? ; - @linkml:Double ? ; + @ ? ; + @ ? ; + @ ? ; + @ ? ; @ ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:Uriorcurie ? ; + @ ? ; @ ? ; @ ? ) ; @@ -2083,7 +3107,64 @@ linkml:Sparqlpath xsd:string ] ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; @ ? ) ; rdf:type [ ] @@ -2102,12 +3183,12 @@ linkml:Sparqlpath xsd:string { ( $ ( @ ? ; - @linkml:Uriorcurie * ; - rdf:type @linkml:String * ; + @ * ; + rdf:type @ * ; rdfs:label @ ? ; dcterms:description @ ? ; @ * ; - @linkml:Boolean ? + @ ? ) ; rdf:type [ ] ) @@ -2131,8 +3212,8 @@ linkml:Sparqlpath xsd:string ] ? ; - @linkml:String * ; - @linkml:Integer ? + @ * ; + @ ? ) ; rdf:type [ ] ) @@ -2149,12 +3230,12 @@ linkml:Sparqlpath xsd:string { ( $ ( rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate @ ; rdf:object @ ; @ ? ; - @linkml:Uriorcurie ? ; - @linkml:Uriorcurie ? ; - @linkml:String * + @ ? ; + @ ? ; + @ * ) ; rdf:type [ ] ? ) @@ -2162,7 +3243,7 @@ linkml:Sparqlpath xsd:string { ( $ ( rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate @ ; rdf:object @ ) ; rdf:type [ ] ? @@ -2176,17 +3257,131 @@ linkml:Sparqlpath xsd:string { ( $ ( & ; rdf:type [ ] ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:String ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; [ ] ? ; - @linkml:Uriorcurie ? ; + @ ? ; @ ? ) ; rdf:type [ ] ? @@ -2196,36 +3391,264 @@ linkml:Sparqlpath xsd:string { ( $ ( & ; rdf:type [ ] ? ; - @linkml:String ? ; - [ - - - ] ? ; - @linkml:String ? ; - [ - - - ] ? ; - @linkml:Uriorcurie ? - ) ; - rdf:type [ ] ? - ) -} - - { - ( $ ( & ; - rdf:type [ ] ? ; - @linkml:String ? ; - [ - - - ] ? ; - @linkml:String ? ; - [ - - - ] ? ; - @linkml:Uriorcurie ? + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; + [ + + + ] ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; + [ + + + ] ? ; + @ ? + ) ; + rdf:type [ ] ? + ) +} + + { + ( $ ( & ; + rdf:type [ ] ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; + [ + + + ] ? ; + [ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] ? ; + [ + + + ] ? ; + @ ? ) ; rdf:type [ ] ? ) @@ -2233,7 +3656,7 @@ linkml:Sparqlpath xsd:string { ( $ ( rdf:subject @ ; - rdf:predicate @linkml:Uriorcurie ; + rdf:predicate @ ; rdf:object @ ) ; rdf:type [ ] ? @@ -2258,8 +3681,8 @@ linkml:Sparqlpath xsd:string ] ? ; - @linkml:String * ; - @linkml:Integer ? + @ * ; + @ ? ) ; rdf:type [ ] ) @@ -2272,10 +3695,10 @@ linkml:Sparqlpath xsd:string rdf:type [ ] ? ; rdf:object @ ; @ ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Double ? ; - @linkml:Double ? + @ ? ; + @ ? ; + @ ? ; + @ ? ) ; rdf:type [ ] ? ) @@ -2382,14 +3805,14 @@ linkml:Sparqlpath xsd:string & ; rdf:type [ ] ? ; @ ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Time ? ; - @linkml:String ? ; - @linkml:String ? + @ ? ; + @ ? ; + @ ? ; + @ ? ; + @ ? ; + @