Fix ENVO import, add ORCIDIO

docs/odk-workflows/RepositoryFileStructure.md

@@ -26,3 +26,8 @@ Components, in contrast to imports, are considered full members of the ontology.
 2. A part of the ontology is managed in ROBOT templates
 3. The expressivity of the component is higher than the format of the edit file. For example, people still choose to manage their ontology in OBO format (they should not) missing out on a lot of owl features. They may choose to manage logic that is beyond OBO in a specific OWL component.
 
+These are the components in FBBI
+
+| Filename | URL |
+| -------- | --- |
+| orcidio.owl | None |

src/ontology/Makefile

@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                2896ea1d0cc1ffaf7742742d22644a31d17bfe0a130e6e37dd4a9babf75985d3
+CONFIG_HASH=                298f0b177bd11c6df8f99fe6755aa350025828149603d6f6ac06eb3ee26ca76d
 
 
 # ----------------------------------------
@@ -57,7 +57,7 @@ OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 
+OTHER_SRC =                 $(COMPONENTSDIR)/orcidio.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
@@ -155,7 +155,7 @@ custom_robot_plugins:
 
 
 .PHONY: extra_robot_plugins
-extra_robot_plugins: 
+extra_robot_plugins:  $(ROBOT_PLUGINS_DIRECTORY)/odk.jar 
 
 
 # Install all ROBOT plugins to the runtime plugins directory
@@ -175,6 +175,9 @@ $(ROBOT_PLUGINS_DIRECTORY)/%.jar:
 
 # Specific rules for supplementary plugins defined in configuration
 
+$(ROBOT_PLUGINS_DIRECTORY)/odk.jar:
+	curl -L -o $@ https://github.com/INCATools/odk-robot-plugin/releases/download/odk-robot-plugin-0.3.3/odk.jar
+
 
 # ----------------------------------------
 # Release assets
@@ -407,7 +410,7 @@ $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(ALL_TERMS) \
 	$(ROBOT) merge --input $< \
 		 extract $(foreach f, $(ALL_TERMS), --term-file $(f)) $(T_IMPORTSEED) \
 		         --force true --copy-ontology-annotations false \
-		         --individuals include \
+		         --individuals exclude \
 		         --method BOT \
 		 remove $(foreach p, $(ANNOTATION_PROPERTIES), --term $(p)) \
 		        $(foreach f, $(ALL_TERMS), --term-file $(f)) $(T_IMPORTSEED) \
@@ -443,6 +446,44 @@ no-mirror-refresh-%:
 	$(MAKE) --assume-new=$(SRC) --assume-new=$(IMPORTDIR)/$*_terms.txt \
 		IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl
 
+# ----------------------------------------
+# Components
+# ----------------------------------------
+# Some ontologies contain external and internal components. A component is included in the ontology in its entirety.
+
+ifeq ($(COMP),true)
+.PHONY: all_components
+all_components: $(OTHER_SRC)
+
+.PHONY: recreate-components
+recreate-components:
+	$(MAKE) --assume-new=$(TMPDIR)/stamp-component-orcidio.owl \
+		COMP=true IMP=false MIR=true PAT=true all_components
+
+.PHONY: no-mirror-recreate-components
+no-mirror-recreate-components:
+	$(MAKE) --assume-new=$(TMPDIR)/stamp-component-orcidio.owl \
+		COMP=true IMP=false MIR=false PAT=true all_components
+
+.PHONY: recreate-%
+recreate-%:
+	$(MAKE) --assume-new=$(TMPDIR)/stamp-component-$*.owl \
+		COMP=true IMP=false MIR=true PAT=true $(COMPONENTSDIR)/$*.owl
+
+.PHONY: no-mirror-recreate-%
+no-mirror-recreate-%:
+	$(MAKE) --assume-new=$(TMPDIR)/stamp-component-$*.owl \
+		COMP=true IMP=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl
+
+$(COMPONENTSDIR)/%.owl: $(TMPDIR)/stamp-component-%.owl | $(COMPONENTSDIR)
+	test -f $@ || touch $@
+.PRECIOUS: $(COMPONENTSDIR)/%.owl
+
+$(TMPDIR)/stamp-component-%.owl: | $(TMPDIR)
+	touch $@
+.PRECIOUS: $(TMPDIR)/stamp-component-%.owl
+
+endif # COMP=true
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

src/ontology/catalog-v001.xml

@@ -2,5 +2,6 @@
 <catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="public">
   <group id="odk-managed-catalog" prefer="public">
     <uri name="http://purl.obolibrary.org/obo/fbbi/imports/merged_import.owl" uri="imports/merged_import.owl" />
+    <uri name="http://purl.obolibrary.org/obo/fbbi/components/orcidio.owl" uri="components/orcidio.owl" />
   </group>
 </catalog>

src/ontology/components/orcidio.owl

@@ -0,0 +1,45 @@
+Prefix(:=<http://purl.obolibrary.org/obo/fbbi/components/orcidio.owl#>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/fbbi/components/orcidio.owl>
+<http://purl.obolibrary.org/obo/fbbi/releases/2026-06-22/components/orcidio.owl>
+Annotation(owl:versionInfo "2026-06-22")
+
+Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9606>))
+Declaration(NamedIndividual(<https://orcid.org/0000-0002-6095-8718>))
+Declaration(NamedIndividual(<https://orcid.org/0000-0002-7073-9172>))
+Declaration(NamedIndividual(<https://orcid.org/0000-0002-8841-5870>))
+Declaration(AnnotationProperty(<http://purl.org/dc/terms/description>))
+Declaration(AnnotationProperty(<http://purl.org/dc/terms/source>))
+
+
+
+############################
+#   Named Individuals
+############################
+
+# Individual: <https://orcid.org/0000-0002-6095-8718> (Damien Goutte-Gattat)
+
+AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q59702685>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0002-6095-8718> "researcher ORCID ID = 0000-0002-6095-8718")
+AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q59702685>) rdfs:label <https://orcid.org/0000-0002-6095-8718> "Damien Goutte-Gattat")
+ClassAssertion(<http://purl.obolibrary.org/obo/NCBITaxon_9606> <https://orcid.org/0000-0002-6095-8718>)
+
+# Individual: <https://orcid.org/0000-0002-7073-9172> (David Osumi-Sutherland)
+
+AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q54303418>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0002-7073-9172> "researcher")
+AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q54303418>) rdfs:label <https://orcid.org/0000-0002-7073-9172> "David Osumi-Sutherland")
+ClassAssertion(<http://purl.obolibrary.org/obo/NCBITaxon_9606> <https://orcid.org/0000-0002-7073-9172>)
+
+# Individual: <https://orcid.org/0000-0002-8841-5870> (Willy W Wong)
+
+AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q57679070>) <http://purl.org/dc/terms/description> <https://orcid.org/0000-0002-8841-5870> "researcher ORCID ID = 0000-0002-8841-5870")
+AnnotationAssertion(Annotation(<http://purl.org/dc/terms/source> <http://www.wikidata.org/entity/Q57679070>) rdfs:label <https://orcid.org/0000-0002-8841-5870> "Willy W Wong")
+ClassAssertion(<http://purl.obolibrary.org/obo/NCBITaxon_9606> <https://orcid.org/0000-0002-8841-5870>)
+
+
+)

src/ontology/fbbi-edit.owl

@@ -7,6 +7,7 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/fbbi.owl>
+Import(<http://purl.obolibrary.org/obo/fbbi/components/orcidio.owl>)
 Import(<http://purl.obolibrary.org/obo/fbbi/imports/merged_import.owl>)
 Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.org/obo/FBbi_root_00000000>)
 Annotation(<http://purl.org/dc/terms/contributor> <https://orcid.org/0000-0002-6095-8718>)

src/ontology/fbbi-odk.yaml

@@ -5,12 +5,20 @@ documentation:
   documentation_system: mkdocs
 namespaces:
   - http://purl.obolibrary.org/obo/FBbi_
+robot_plugins:
+  plugins:
+    - name: odk
+      mirror_from: https://github.com/INCATools/odk-robot-plugin/releases/download/odk-robot-plugin-0.3.3/odk.jar
 import_group:
   use_base_merging: true
+  slme_individuals: exclude
   products:
   - id: ro
   - id: omo
   - id: iao
+components:
+  products:
+  - filename: orcidio.owl
 robot:
   reasoner: ELK
 repo: fbbi

src/ontology/fbbi.Makefile

@@ -3,3 +3,11 @@
 ## If you need to customize your Makefile, make
 ## changes here rather than in the main Makefile
 
+# Automatically generate the orcidio component from ORCID references
+# within the ontology.
+# Of note, ODK 1.7 will have built-in support for this, so once ODK 1.7
+# is out we should replace this with the built-in feature.
+$(COMPONENTSDIR)/orcidio.owl: $(TMPDIR)/stamp-component-%.owl $(EDIT_PREPROCESSED) | $(COMPONENTSDIR) all_robot_plugins
+	$(ROBOT) remove --input $(EDIT_PREPROCESSED) --select imports --trim false \
+		 odk:extract-orcids \
+		 $(ANNOTATE_CONVERT_FILE)