Merge pull request #3185 from obophenotype/componentize-disjoint_unio…

…n_over Turn `disjoint_union_over` into a proper ODK component
obophenotype · Jan 17, 2024 · 632c46c · 632c46c
2 parents 73ec1da + b837ad6
commit 632c46c
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Showing 6 changed files with 13 additions and 11 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -51,7 +51,7 @@ 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 =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-subset.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/vasculature_class.owl $(COMPONENTSDIR)/hra_depiction_3d_images.owl 
+OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/disjoint_union_over.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-subset.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/vasculature_class.owl $(COMPONENTSDIR)/hra_depiction_3d_images.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 PATTERNDIR=                 ../patterns
@@ -402,6 +402,7 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 
 
 
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -44,6 +44,7 @@
       <uri name="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbls.owl" uri="bridge/uberon-bridge-to-wbls.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-xao.owl" uri="bridge/uberon-bridge-to-xao.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/components/develops-from-chains.owl" uri="components/develops-from-chains.owl"/>
+      <uri name="http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl" uri="components/disjoint_union_over.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/hra_subset.owl" uri="components/hra_subset.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/components/in-subset.owl" uri="components/in-subset.owl"/>

diff --git a/...tology/components/disjoint_union_over.ofn → ...tology/components/disjoint_union_over.owl b/...tology/components/disjoint_union_over.ofn → ...tology/components/disjoint_union_over.owl
@@ -6,7 +6,7 @@ Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
 Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
-Ontology(<http://purl.obolibrary.org/obo/uberon/disjoint_union_over.owl>
+Ontology(<http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl>
 
 
 EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000009>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000344>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002072>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002097>)) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0012125>))
@@ -47,4 +47,4 @@ DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050
 DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0010230>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0035639>))
 DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0010419>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0034941>))
 DisjointClasses(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0036072>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0036073>))
-)
+)
diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo
@@ -56,6 +56,7 @@ treat-xrefs-as-is_a: BFO
 treat-xrefs-as-is_a: VHOG
 remark: Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found.
 import: http://purl.obolibrary.org/obo/uberon/components/develops-from-chains.owl
+import: http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl
 import: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl
 import: http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl
 import: http://purl.obolibrary.org/obo/uberon/components/in-subset.owl

diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml
@@ -127,6 +127,7 @@ documentation:
   documentation_system: mkdocs
 components:
   products:
+    - filename: disjoint_union_over.owl
     - filename: mappings.owl
     - filename: in-subset.owl
     - filename: hra_subset.owl

diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile
@@ -136,15 +136,13 @@ $(TMPDIR)/plugins/uberon.jar:
 # BUILDING UBERON ITSELF
 # ----------------------------------------
 
-# Step 1: Preprocessing. We Merge the edit file file with imports,
-# disjointness axioms, and list of contributors, then expand macros
-# (except RO:0002175, which only needs to be expanded for QC purposes).
-$(OWLSRC): $(SRC) $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv
+# Step 1: Preprocessing. We Merge the edit file file with imports and
+# list of contributors, then expand macros (except RO:0002175, which
+# only needs to be expanded for QC purposes).
+$(OWLSRC): $(SRC) $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv
 	@echo "STRONG WARNING: issues/contributor.owl needs to be manually updated."
-	$(ROBOT) merge -i $< \
-			-i $(COMPONENTSDIR)/disjoint_union_over.ofn \
-			-i issues/contributor.owl \
-		expand --no-expand-term http://purl.obolibrary.org/obo/RO_0002175 \
+	$(ROBOT) merge -i $< -i issues/contributor.owl \
+		 expand --no-expand-term http://purl.obolibrary.org/obo/RO_0002175 \
 			-o $@
 
 # Step 2: Reasoning.