Merge branch 'master' into pr/cthoyt/3082

obophenotype · Oct 26, 2023 · c152fda · c152fda
2 parents 85b5753 + 3d04ccf
commit c152fda
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diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -28,6 +28,7 @@ These are the current imports in UBERON
 | 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 |
+| omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
 
 ## 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:

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -114,7 +114,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  pr cl go envo ro bspo chebi pato bfo ncbitaxon nbo orcidio
+IMPORTS =  pr cl go envo ro bspo chebi pato bfo ncbitaxon nbo orcidio omo
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -339,6 +339,12 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/%_terms_combined
 
 .PRECIOUS: $(IMPORTDIR)/%_import.owl
 
+## Module for ontology: omo
+
+$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/omo_terms_combined.txt
+	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru  \
+    $(ANNOTATE_CONVERT_FILE); fi
+
 
 .PHONY: refresh-imports
 refresh-imports:
@@ -427,8 +433,9 @@ mirror-cl: | $(TMPDIR)
 .PHONY: mirror-go
 .PRECIOUS: $(MIRRORDIR)/go.owl
 mirror-go: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/go/go-base.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/go/go-base.owl -o $@.tmp.owl && \
+		$(ROBOT) remove -i $@.tmp.owl --base-iri http://purl.obolibrary.org/obo/GO_ --base-iri http://purl.obolibrary.org/obo/GOREL_ --base-iri http://purl.obolibrary.org/obo/GOCHE_ --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: envo
@@ -504,6 +511,15 @@ 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
 
+
+## ONTOLOGY: omo
+.PHONY: mirror-omo
+.PRECIOUS: $(MIRRORDIR)/omo.owl
+mirror-omo: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o $@.tmp.owl &&\
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+
 ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
 MERGE_MIRRORS = true
 

diff --git a/src/ontology/imports/local-cteno.owl b/src/ontology/imports/local-cteno.owl
@@ -12857,12 +12857,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/UBERON_0006846 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0006846">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0003102"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">surface groove</rdfs:label>
-    </owl:Class>
 
 
 

diff --git a/src/ontology/imports/local-ehdaa2.owl b/src/ontology/imports/local-ehdaa2.owl
@@ -25905,7 +25905,6 @@ SubClassOf(<http://purl.obolibrary.org/obo/EHDAA2_0004738> ObjectSomeValuesFrom(
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/EHDAA2_0004739> "extraembryonic coelum"^^xsd:string)
 SubClassOf(<http://purl.obolibrary.org/obo/EHDAA2_0004739> <http://purl.obolibrary.org/obo/AEO_0000221>)
 SubClassOf(<http://purl.obolibrary.org/obo/EHDAA2_0004739> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0001025> <http://purl.obolibrary.org/obo/EHDAA2_0000472>))
-SubClassOf(<http://purl.obolibrary.org/obo/EHDAA2_0004739> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002371> <http://purl.obolibrary.org/obo/EHDAA2_0000267>))
 SubClassOf(<http://purl.obolibrary.org/obo/EHDAA2_0004739> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002496> <http://purl.obolibrary.org/obo/HsapDv_0000016>))
 
 # Class: <http://purl.obolibrary.org/obo/EHDAA2_0004740> (urogenital sinus epithelium vesical part)
@@ -26330,4 +26329,4 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.ob
 AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/ZFA_0001690> "true"^^xsd:boolean)
 
 
-)
+)