Merge branch 'master' into fix-bridge-generation

.github/workflows/qc.yml

@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.4.1
+    container: obolibrary/odkfull:v1.4.3
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -30,7 +30,7 @@ jobs:
         env:
           DEFAULT_BRANCH: master
           ROBOT_JAVA_ARGS: -Xmx6G
-        run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' BRI=false MIR=false IMP=false test > TESTLOG.log
+        run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' GH_ACTION=true BRI=false MIR=false IMP=false test > TESTLOG.log
       - name: Last rows of QC report
         if: ${{ failure() }}
         run: tail -20 src/ontology/TESTLOG.log

docs/odk-workflows/RepositoryFileStructure.md

@@ -27,6 +27,7 @@ These are the current imports in UBERON
 | bfo | http://purl.obolibrary.org/obo/bfo.owl | None |
 | ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
 | nbo | http://purl.obolibrary.org/obo/nbo.owl | None |
+| orcidio | https://w3id.org/orcidio/orcidio.owl | None |
 
 ## Components
 Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for uberon
 # Generated using ontology-development-kit
-# ODK Version: v1.4.1
+# ODK Version: v1.4.3
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead
 
@@ -44,7 +44,7 @@ REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy id-format 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.4.1
+ODK_VERSION_MAKEFILE =      v1.4.3
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -114,7 +114,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  pr cl go envo ro bspo chebi pato bfo ncbitaxon nbo
+IMPORTS =  pr cl go envo ro bspo chebi pato bfo ncbitaxon nbo orcidio
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -496,6 +496,14 @@ mirror-nbo: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/nbo/nbo-base.owl --create-dirs -o $(MIRRORDIR)/nbo.owl --retry 4 --max-time 200 &&\
 		$(ROBOT) convert -i $(MIRRORDIR)/nbo.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
+
+## ONTOLOGY: orcidio
+.PHONY: mirror-orcidio
+.PRECIOUS: $(MIRRORDIR)/orcidio.owl
+mirror-orcidio: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://w3id.org/orcidio/orcidio.owl -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+
 ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
 MERGE_MIRRORS = true
 

src/ontology/catalog-v001.xml

@@ -49,6 +49,7 @@
       <uri name="http://purl.obolibrary.org/obo/wbls.owl" uri="imports/local-wbls.owl"/>
       <uri name="http://purl.obolibrary.org/obo/xao.owl" uri="imports/local-xao.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl" uri="components/hra_subset.owl"/>
+      <uri name="http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl" uri="components/hra_depiction_3d_images.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/components/in-subset.owl" uri="components/in-subset.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/components/mappings.owl" uri="components/mappings.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/components/vasculature_class.owl" uri="components/vasculature_class.owl"/>

src/ontology/uberon-odk.yaml

@@ -65,6 +65,10 @@ import_group:
       mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl
     - id: nbo
       use_base: TRUE
+    - id: orcidio
+      mirror_from: https://w3id.org/orcidio/orcidio.owl
+      base_iris:
+        - https://orcid.org/
 subset_group:
   products:
     - id: appendicular-minimal

src/ontology/uberon.Makefile

@@ -140,11 +140,18 @@ $(OWLSRC): $(SRC) $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-g
 # For the temporary injection of property chains, see
 # <https://github.com/obophenotype/uberon/issues/2381>
 DEVELOPS_FROM_CHAIN=$(COMPONENTSDIR)/develops-from-chains.owl
+# The 'materialize' step is too resource-intensive for the GitHub
+# Action runners, so we leave it out when running online QC checks, see
+# <https://github.com/obophenotype/uberon/pull/3087#issuecomment-1755553647>
+ifeq ($(GH_ACTION),true)
+MATERIALIZE=
+else
+MATERIALIZE = materialize -T $(CONFIGDIR)/basic_properties.txt -r elk
+endif
 uberon.owl: $(OWLSRC) $(BRIDGEDIR)/uberon-bridge-to-bfo.owl $(DEVELOPS_FROM_CHAIN)
 	$(ROBOT) merge -i $(OWLSRC) -i $(BRIDGEDIR)/uberon-bridge-to-bfo.owl \
 	               -i $(DEVELOPS_FROM_CHAIN) \
-	         relax \
-	         materialize -T $(CONFIGDIR)/basic_properties.txt -r elk \
+	         relax $(MATERIALIZE) \
 	         reason -r elk --exclude-duplicate-axioms true \
 	                       --equivalent-classes-allowed asserted-only \
 	         unmerge -i $(DEVELOPS_FROM_CHAIN) \