diff --git a/src/biolink_model/schema/biolink_model.yaml b/src/biolink_model/schema/biolink_model.yaml index ad8529118..cecd4e81e 100644 --- a/src/biolink_model/schema/biolink_model.yaml +++ b/src/biolink_model/schema/biolink_model.yaml @@ -109,6 +109,7 @@ prefixes: NDDF: 'http://purl.bioontology.org/ontology/NDDF/' NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=' OBAN: 'http://purl.org/oban/' + OBA: 'http://purl.obolibrary.org/obo/OBA_' OMIM.PS: 'https://www.omim.org/phenotypicSeries/' ORCID: 'https://orcid.org/' orphanet: 'http://www.orpha.net/ORDO/Orphanet_' @@ -147,6 +148,7 @@ prefixes: VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/' UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#' VMC: 'https://github.com/ga4gh/vr-spec/' + VT: 'http://purl.obolibrary.org/obo/VT_' WBls: 'http://purl.obolibrary.org/obo/WBls_' WBbt: 'http://purl.obolibrary.org/obo/WBbt_' WBVocab: 'http://bio2rdf.org/wormbase_vocabulary' @@ -6626,6 +6628,53 @@ classes: examples: - value: CHEBI:35469 # antidepressant role + biological attribute: + aliases: ['trait', 'biological trait', 'organismal attribute'] + is_a: attribute + description: >- + A measurable or observable characteristic of a biological entity, organism, or part of an + organism that describes an inherent or acquired feature without reference to a specific + abnormal or pathological state. Biological attributes can include anatomical properties + (e.g., size, shape, color), physiological measurements (e.g., blood glucose level, metabolic + rate), or behavioral characteristics. Unlike phenotypic features, which may emphasize deviation + from normal states, biological attributes represent neutral descriptors that can be measured + or observed across populations. These attributes form the basis for quantitative trait loci + (QTL) and genome-wide association studies (GWAS), where they serve as the traits being mapped + to genetic variants. + comments: + - >- + Biological attributes differ from phenotypic features in that they represent + generic, measurable characteristics without an inherent notion of abnormality. + For example, 'lysine in blood amount' is a biological attribute, while 'hypolysinemia' + (decreased blood lysine) is a phenotypic feature that denotes deviation from normal. + - >- + OBA terms use the Entity-Quality (EQ) pattern, combining entities (from ontologies + like UBERON, ChEBI, GO, CL) with qualities (from PATO) to create composite biological + attributes. + examples: + - value: OBA:2020005 + description: lysine in blood amount + - value: OBA:0002360 + description: trochanter size + - value: OBA:VT0000188 + description: blood glucose amount + - value: OBA:VT0000047 + description: head circumference + - value: OBA:0002294 + description: brain ventricle size + exact_mappings: + - OBA:0000001 # biological attribute (root term) + broad_mappings: + - PATO:0000001 # characteristic + related_mappings: + - SIO:000614 # attribute (already mapped to parent class) + id_prefixes: + - OBA + - VT # Vertebrate Trait Ontology (integrated into OBA) + see_also: + - https://github.com/obophenotype/bio-attribute-ontology + - https://pubmed.ncbi.nlm.nih.gov/36747660/ + biological sex: is_a: attribute exact_mappings: